How to stick table header(thead) on top while scrolling down the table rows with fixed header(navbar) in bootstrap 3?

This can now be done without JS, just pure CSS. So, anyone trying to do this for modern browsers should look into using position: sticky instead.

Currently, both Edge and Chrome have a bug where position: sticky doesn't work on thead or tr elements, however it's possible to use it on th elements, so all you need to do is just add this to your code:

th {
  position: sticky;
  top: 50px;  /* 0px if you don't have a navbar, but something is required */
  background: white;
}

Note: you'll need a background color for them, or you'll be able to see through the sticky title bar.

This has very good browser support.

Demo with your code (HTML unaltered, above 5 lines of CSS added, all JS removed):

body {
    padding-top:50px;
}
table.floatThead-table {
    border-top: none;
    border-bottom: none;
    background-color: #fff;
}

th {
  position: sticky;
  top: 50px;
  background: white;
}
<link rel="stylesheet" type="text/css" href="//netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css">

<!-- Fixed navbar -->
<div class="navbar navbar-default navbar-fixed-top">
    <div class="container">
        <div class="navbar-header">
            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> <span class="icon-bar"></span>
 <span class="icon-bar"></span>
 <span class="icon-bar"></span>

            </button> <a class="navbar-brand" href="#">Project name</a>

        </div>
        <div class="collapse navbar-collapse">
            <ul class="nav navbar-nav">
                <li class="active"><a href="#">Home</a>

                </li>
                <li><a href="#about">About</a>

                </li>
                <li><a href="#contact">Contact</a>

                </li>
                <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <b class="caret"></b></a>

                    <ul class="dropdown-menu">
                        <li><a href="#">Action</a>

                        </li>
                        <li><a href="#">Another action</a>

                        </li>
                        <li><a href="#">Something else here</a>

                        </li>
                        <li class="divider"></li>
                        <li class="dropdown-header">Nav header</li>
                        <li><a href="#">Separated link</a>

                        </li>
                        <li><a href="#">One more separated link</a>

                        </li>
                    </ul>
                </li>
            </ul>
        </div>
        <!--/.nav-collapse -->
    </div>
</div>
<!-- Begin page content -->
<div class="container">
    <div class="page-header">
         <h1>Sticky Table Headers</h1>

    </div>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <table class="table table-striped sticky-header">
        <thead>
            <tr>
                <th>#</th>
                <th>First Name</th>
                <th>Last Name</th>
                <th>Username</th>
            </tr>
        </thead>
        <tbody>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
        </tbody>
    </table>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
    <p class="lead">If the page is tall and all of the table is visible, then it won't stick. Make your viewport short.</p>
     <h3>Table 2</h3>

    <table class="table table-striped sticky-header">
        <thead>
            <tr>
                <th>#</th>
                <th>New Table</th>
                <th>Last Name</th>
                <th>Username</th>
            </tr>
        </thead>
        <tbody>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
            <tr>
                <td>1</td>
                <td>Mark</td>
                <td>Otto</td>
                <td>@mdo</td>
            </tr>
            <tr>
                <td>2</td>
                <td>Jacob</td>
                <td>Thornton</td>
                <td>@fat</td>
            </tr>
            <tr>
                <td>3</td>
                <td>Larry</td>
                <td>the Bird</td>
                <td>@twitter</td>
            </tr>
        </tbody>
    </table>
</div>


Use: https://github.com/mkoryak/floatThead

Docs: http://mkoryak.github.io/floatThead/examples/bootstrap3/

$(document).ready(function(){
  $(".sticky-header").floatThead({top:50});
});

DEMO with 2 Tables and Fixed Header: http://jsbin.com/zuzuqe/1/

http://jsbin.com/zuzuqe/1/edit


HTML

<!-- Fixed navbar -->
<div class="navbar navbar-default navbar-fixed-top">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <a class="navbar-brand" href="#">Project name</a>
    </div>
    <div class="collapse navbar-collapse">
      <ul class="nav navbar-nav">
        <li class="active"><a href="#">Home</a></li>
        <li><a href="#about">About</a></li>
        <li><a href="#contact">Contact</a></li>
        <li class="dropdown">
          <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <b class="caret"></b></a>
          <ul class="dropdown-menu">
            <li><a href="#">Action</a></li>
            <li><a href="#">Another action</a></li>
            <li><a href="#">Something else here</a></li>
            <li class="divider"></li>
            <li class="dropdown-header">Nav header</li>
            <li><a href="#">Separated link</a></li>
            <li><a href="#">One more separated link</a></li>
          </ul>
        </li>
      </ul>
    </div>
    <!--/.nav-collapse -->
  </div>
</div>

<!-- Begin page content -->
<div class="container">
  <div class="page-header">
    <h1>Sticky footer with fixed navbar</h1>
  </div>
  <p class="lead">Pin a fixed-height footer to the bottom of the viewport in desktop browsers with this custom HTML and CSS. A fixed navbar has been added within <code>#wrap</code> with <code>padding-top: 60px;</code> on the <code>.container</code>.</p>
  <table class="table table-striped sticky-header">
    <thead>
      <tr>
        <th>#</th>
        <th>First Name</th>
        <th>Last Name</th>
        <th>Username</th>
      </tr>
    </thead>
    <tbody>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
    </tbody>
  </table>

  <h3>Table 2</h3>

  <table class="table table-striped sticky-header">
    <thead>
      <tr>
        <th>#</th>
        <th>New Table</th>
        <th>Last Name</th>
        <th>Username</th>
      </tr>
    </thead>
    <tbody>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
      <tr>
        <td>1</td>
        <td>Mark</td>
        <td>Otto</td>
        <td>@mdo</td>
      </tr>
      <tr>
        <td>2</td>
        <td>Jacob</td>
        <td>Thornton</td>
        <td>@fat</td>
      </tr>
      <tr>
        <td>3</td>
        <td>Larry</td>
        <td>the Bird</td>
        <td>@twitter</td>
      </tr>
    </tbody>
  </table>
</div>

CSS

body{
  padding-top:50px;
}
table.floatThead-table {
  border-top: none;
  border-bottom: none;
  background-color: #fff;
}

You can do it easily with puse CSS without any kind of JS. you have to add position: sticky; top: 0; z-index:999; in table th . But this won't work on Chrome Browser but other browser. To work on chrome you have to add those code in table thead th

.table-fixed {
  width: 100%;
}

/*This will work on every browser but Chrome Browser*/
.table-fixed thead {
  position: sticky;
  position: -webkit-sticky;
  top: 0;
  z-index: 999;
  background-color: #000;
  color: #fff;
}

/*This will work on every browser*/
.table-fixed thead th {
    position: sticky;
    position: -webkit-sticky;
    top: 0;
    z-index: 999;
    background-color: #000;
    color: #fff;
}
<table class="table-fixed">
  <thead>
    <tr>
        <th>Table Header 1</th>
        <th>Table Header 2</th>
        <th>Table Header 3</th>
    </tr>
  </thead>
  <tbody>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
    <tr>
        <td>Data</td>
        <td>Data</td>
        <td>Data</td>
    </tr>
  </tbody>
</table>