They're the same. The difference, at is omitted in [1]:
[1] What time are you leaving (at)?
[2] At what time are you leaving?
There's a Latin rule borrowed into English that states, one should never end a sentence with a preposition. The result, some speakers move the preposition to the front of the clause ([2]), other speakers omit (1), and yet other speakers just leave it where it is. The result, three ways to say the same thing:
Statement: I am leaving at 4 p.m.
Questions:
What time are you leaving at?
At what time are you leaving?
What time are you leaving?
Does that help?