Heard something similar in my old place in Rugeley years back. Turned out to be a pine marten but I still spent two hours up there with a torch convinced I was going to find something I'd regret. You never quite shake that 3am feeling do you.
Worth ruling out the boring stuff first - thermal expansion of roof joists can actually sound surprisingly loud and rhythmic, almost deliberate. Old houses are terrible for it.
But if it happens again at the same time, multiple nights, that changes things. 3am has a bit of a reputation for a reason and I'm not talking wildlife. What kind of house is it, how old roughly? That matters more than people think.