Did you see it in daytime? For every rat you see in daytime there are at least 20 more. It is rare to see them out in the day and only the very bold ones do it.
I know someone who had rats burrow into the rabbits' pen and lived there. The owners had no idea until they saw 3 sets of eyes in the run one night. They dug the whole place up and found a nest with loads. Unfortunately a rabbit got bitten, it was very ill and went mentally ill too and cant remember fully but I think it had to get put down.
Do you have a dog? When our entire street got infested with rats (they dug up a sewer opposite) the rat-catcher said that the only reason we didnt have them in the house was because of the dogs, they act as a deterrent.
We did have them in the stables and garden though. The buns didnt get ill, but I think the rats were wary of them as we had a group of over 10 bunnies at the time. We did find a dead rat in there one morning though, and a nest of kits missing
We tried traps but they were too smart for it, by the time we had caught one, another litter of rats would have been born. They put rabbits to shame in the breeding category.
Moral of these stories - dont let it/them get established, nip it in the bud. Call a professional asap and ask which method of getting rid would be best in your circumstances.