Has Thor fought with himself from a different timeline?

It depends what you mean by Thor fighting himself from a different timeline. Since you mentioned time travel in your question, it sounds to me like you're asking whether the real Thor Odinson ever fought an older or younger version of himself from the past or the future. And if that's what you meant, then I don't believe a fight like that has ever happened.

We did see the real Thor meet an older version of himself, and later a younger version of himself as well, but they didn't fight one another, opting to team up instead.

Thor: God of Thunder Vol 1 #5

Thor: God of Thunder Vol 1 #8

Thor Vol 5 #14

Apparently, the Russo brothers planned to have a fight scene between the present and past Thor in Avengers: Endgame, but they had a change of heart and decided not to go with that.

If you count Thor Odinson fighting other versions of himself from alternate universes (with no time travel involved), then there've been two instances that I'm aware of. In the first instance, the Thor Odinson of Earth 616 (the Thor of the prime Marvel universe, who was known as Unworthy Thor at the time) fought the Thor Odinson of Earth-1610 (AKA, Ultimate Thor).

Thors Vol 1 #2

And in the second instance (which Raj cited in his answer), Ultimate Thor fought the Thor of Earth-16001 (AKA, Rune Thor). They had two fights, in fact, in consecutive issues, but the following image is from the first.

Thors Vol 1 #3

If you're willing to count Thor Odinson fighting other people who wielded his powers and used his name, then there've been several instances of that.

Thor vs. 'Thor' (Red Norvell) - Thor Vol 1 #478

Thor vs. 'Thor' (Eric Masterson) - Thor Vol 1 #459

Thor vs. 'Thor' (Jane Foster) - Thor Vol 4 #4

Thor Odinson has also had multiple fights with Beta Ray Bill, who doesn't typically use his name, but does wield his powers.

Thor Vol 1 #472

If you're willing to count other people with Thor's powers fighting each other, then there've been at least a couple of instances of that as well.

'Thor' (Eric Masterson) vs. 'Thor' (Dargo Ktor) - Thor Vol 1 #439 (also cited in Raj's answer)

'Thor' (Jane Foster) vs. 'War Thor' (Volstagg) - Mighty Thor Vol 2 #23

I'm fairly sure the last half-dozen examples weren't really the sort of thing you had in mind, but just in case I'm wrong about that, I decided to include them anyway.