I have two cats and three litter boxes. I second RoJo's suggestion to get at least one more box, if you have only one.
One of my cats tended to pee in wrong places because she hated the litter (I used pellets and as it later turned out, she prefers sand-like clay). Maybe that's an option worth checking.
Buy special liquid for removing cat pee (should be in your pet shop). Even if you think there's no smell left, your cat could detect and pee smell means "here's my toilet". Those washing liquids break down the substances of the pee on the chemical level, completely removing the smell even for the cat.
If you cat has problem with urinary tract and feels pain when peeing, he/she tries to avoid the place where it hurts = the litter box, because he/she associates the pain with the box. You may want to take a sample of the cat's urine and test it at the vet.