How can I delete using INNER JOIN with SQL Server?

Try this:

DELETE FROM WorkRecord2 
       FROM Employee 
Where EmployeeRun=EmployeeNo
      And Company = '1' 
      AND Date = '2013-05-06'

It is possible this will be helpful for you -

DELETE FROM dbo.WorkRecord2
WHERE EmployeeRun IN (
    SELECT e.EmployeeNo
    FROM dbo.Employee e
    WHERE ...
)

Or try this -

DELETE FROM dbo.WorkRecord2
WHERE EXISTS(
    SELECT 1
    FROM dbo.Employee e
    WHERE EmployeeRun = e.EmployeeNo
        AND ....
)

Just add the name of the table between DELETE and FROM from where you want to delete records, because we have to specify the table to delete. Also remove the ORDER BY clause because there is nothing to order while deleting records.

So your final query should be like this:

    DELETE WorkRecord2 
      FROM WorkRecord2 
INNER JOIN Employee 
        ON EmployeeRun=EmployeeNo
     WHERE Company = '1' 
       AND Date = '2013-05-06';

You need to specify what table you are deleting from. Here is a version with an alias:

DELETE w
FROM WorkRecord2 w
INNER JOIN Employee e
  ON EmployeeRun=EmployeeNo
WHERE Company = '1' AND Date = '2013-05-06'