[mesmark]

Yes.

When you use 'by' you are saying 'before time runs out'.

Hand in that report by the end of the day tomorrow.
(You have until that time or it's late/too late.)

Whe you use 'at' you are talking about that specific time.

Hand in that report at the end of the day tomorrow.
(hand it in tomorrow at 5:00, not now.)