In the end.
This refers to a time period. As Jio points out in this answer, it's pretty much synonymous with finally.
The Collins dictionary defines it as - the final result of a series of events, or what is your final conclusion after considering all the relevant facts.
At the end.
Refers to a position. This doesn't just need to be a physical position though: one can be at the end of their life.
To bring this back to your question, it really depends on the context. I.e. What you are at/in the end of.
For example: You have just given a presentation - therefore your location in the timescale of the presentation is at the end.
We are at the end now. Does anyone have any questions?
Or you ask where the snacks are:
They're over there on the table, at the end.
Imagine that you are summarising that presentation though, as I am about to do with this answer - this is a conclusion which considers the facts:
In the end, there is only a subtle difference between the two phrases.
Here is a link from the Merriam Webster Dictionary with more information.