You can't easily control the order things will happen when SQL Server looks at the query you wrote and then determines the optimal execution plan. It won't always produce a plan that follows the same logic you typed, in the same order.
In this case, in order to find the rows you're looking for, SQL Server has to perform two filters:
- identify only the rows that match your variable
- identify only the rows that are numeric
It can do this in either order, so this is also valid:
- identify only the rows that are numeric
- identify only the rows that match your variable
If you look at the properties of this execution plan, you see that the predicate for the match to your variable is listed first (which still doesn't guarantee order of operation), but in any case, due to data type precedence, it has to try to convert the column data to the type of the variable:

Subqueries, CTEs, or writing the query a different way - especially in simple cases like this - are unlikely to change the order SQL Server uses to perform those operations.
You can force evaluation order in most scenarios by using a CASE expression (you also don't need the subquery):
SELECT EmployeeID
FROM #tmp
WHERE EmployeeID = CASE IsNumeric(EmployeeID) WHEN 1 THEN @eid END;
In modern versions of SQL Server (you forgot to tell us which version you use), you can also use TRY_CONVERT() instead:
SELECT EmployeeID
FROM #tmp
WHERE TRY_CONVERT(int, EmployeeID) = @eid;
This is essentially shorthand for the CASE expression, but with the added bonus that it allows you to specify an explicit type, which is one of the downsides of ISNUMERIC(). All ISNUMERIC() tells you is if the value can be converted to any numeric type. The string '1e2' passes the ISNUMERIC() check, because it can be converted to float, but try converting that to an int...
For completeness, the best solution - if there is an index on EmployeeID - is to just use a variable that matches the column data type, as you suggested.
But even better would be to use a data type that prevents junk data like 'aa1234' from getting into the table in the first place.
SELECT EmployeeID FROM #tmp WHERE ISNUMERIC(EmployeeID) = 1 AND EmployeeID = @eid- iSR5