There are rabbits that naturally begin using litter boxes, but most times, it requires a bit of hands on training.
I’d recommend blocking out some of your time to observe your rabbit in an enclosed space with a litter box. Every time your rabbit poos or pees outside the box, pick him up and put him in the litter box, then praise him with a pet and a positive affirmation statement, like good boy. Keep doing this. If there is anything he goes in and uses it on his own, ultra praise him. Stay away from treats or he may associate using the bathroom with getting treats.
Clean up accidents as soon as you can. It is also helpful to establish a sound you can make immediately once an accident happens. Immediacy after an accident is key to learning, and sometimes it happens away from you so you can’t get to him right away. Having a short sound helps (like clicker trainer).
With Wick, it was:
1) Wick pees.
2) I notice and do a short hiss sound.
3) I pick him up and put him in his litter box.
4) I pet and praise him.
Rabbits poo on the fly, so you can’t really predict poos, but rabbits tend to back up and perk their butt up when they’re about to pee. If you suspect he’s going to go pee, don’t wait until he goes. Just pick him up and put him in the box and wait. You can’t implement this until the association is in place and you have a good handle on how he looks when he’s about to pee. Wick’s easy as he sticks his tail up when he has one ready to go.
I hope this helps! Do multiple sessions as often as you can! Patience is key. Neutering will help as well.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.