Is this negative?

[Squarinup]

Very close to a colleague, who recently confided in a few of his about some mental health struggles he has experienced and really opened up. He is very confident and a great guy, have always admired him. I responded saying I could relate and was always there for him. He replied that he really appreciated it, and had “sensed that I’d always had my own battles” - what does this mean? It’s made me a tad paranoid

I'd take that to mean he's perceieved that you've also been through some difficult experiences; perhaps similar to his own. You said that you "could relate" which makes it sound like that is true, and perhaps led him to feel comfortable making the comment...? What's bothered you about it?

You've said you could relate and he's said I thought you might basically. Not a bad thing at all.