Callback of .animate() gets called twice jquery

animate calls its callback once for each element in the set you call animate on:

If supplied, the start, step, progress, complete, done, fail, and always callbacks are called on a per-element basis...

Since you're animating two elements (the html element, and the body element), you're getting two callbacks. (For anyone wondering why the OP is animating two elements, it's because the animation works on body on some browsers but on html on other browsers.)

To get a single callback when the animation is complete, the animate docs point you at using the promise method to get a promise for the animation queue, then using then to queue the callback:

$("html, body").animate(/*...*/)
    .promise().then(function() {
        // Animation complete
    });

(Note: Kevin B pointed this out in his answer when the question was first asked. I didn't until four years later when I noticed it was missing, added it, and...then saw Kevin's answer. Please give his answer the love it deserves. I figured as this is the accepted answer, I should leave it in.)

Here's an example showing both the individual element callbacks, and the overall completion callback:

jQuery(function($) {

  $("#one, #two").animate({
    marginLeft: "30em"
  }, function() {
    // Called per element
    display("Done animating " + this.id);
  }).promise().then(function() {
    // Called when the animation in total is complete
    display("Done with animation");
  });

  function display(msg) {
    $("<p>").html(msg).appendTo(document.body);
  }
});

<div id="one">I'm one</div>
<div id="two">I'm two</div>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>

To get a single callback for the completion of multiple element animations, use deferred objects.

$(".myClass").animate({
  marginLeft: "30em"
}).promise().done(function(){
  alert("Done animating");
});

When you call .animate on a collection, each element in the collection is animated individually. When each one is done, the callback is called. This means if you animate eight elements, you'll get eight callbacks. The .promise().done(...) solution instead gives you a single callback when all animations on those eight elements are complete. This does have a side-effect in that if there are any other animations occurring on any of those eight elements the callback won't occur until those animations are done as well.

See the jQuery API for detailed description of the Promise and Deferred Objects.