What are you cleaning with? A enzymatic pet cleaner is your best bet to eliminate the smell.
Some more suggestions:
He may want separate boxes for peeing and pooping. I would try adding another box. If you have a covered box, I'd get an uncovered. Maybe try Cat Attract brand litter--it is scented to attract cats to it especially for this purpose.
How long have you had the kitten? A 3 month old kitten may not be the greatest at remembering where the box is, especially if he is a recent addition. He may need a couple extra boxes in various locations in the house for a few weeks (I had to do this with my Holly when I first got her).
You may also need to confine him to one small room (e.g. a bathroom) for a few days so he gets the idea.
And if he hasn't been to the vet, a check up would be advisable.
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Holly, Misty & their friend, Jake, the dog.
Onyx, Callie May, Maggie & Kobi forever in my heart.
Yes, I know I need a new signature pic...someday...