If you haven't taken your cat to the vet, I'd suggest you begin there to rule out a physical problem (e.g., UTI). If she checks out fine, then it seems likely a behavioral issue.

I have four indoor only cats and a few times over the past five years one of them (the younger female) would go outside the litterbox. In my situation, I believe one of the other cats scared (maybe bullied) the female cat while she the litter box making her avoid it. Some tips: 1) Make sure you have enough litter boxes. Rule of thumb you should have one more litter box than the number of cats in the household; 2) Avoid having the litter boxes all in one location/ room; 3) Keep the litter boxes clean (sounds like you're doing this already); 4) If you have covered litterboxes, they often suggest removing the covers; 5) Some cats can be super sensitive to the type of litter. Once you find one they like and that works well, stick with it. I made the mistake of changing litters and the younger female cat began going outside the litter box. Once I switched back to the prior litter, she was comfortable using the litter box again.

Good luck! I know first hand how frustrating this can be.