This idiom or expression means:

Having something other than the obvious in mind.
Doing things for reasons other than what is announced.

A. I don’t know why Fred is suddenly interested in helping the poor!
B. He has a personal agenda. It’s not as if he is suddenly a different man!

Also see:
Having an axe to grind.

This idiom or expression can have the following meanings:

Having a grudge:
He has an axe to grind with his ex wife.

Having a personal or hidden reason:
If he’s offering to help you with your situation for no apparent reason, he must have an axe to grind.

Also see:
Having an agenda.