Litter boxes made for cats are fine, but the front of the box should have a low, wide opening, because rabbits often like to back in the litter box as opposed to jumping in. Triangle-shaped boxes designed for the corner of the cage are great space savers.
Line the box with shredded newspaper, hay, recycled-paper pulp and other rabbit-friendly litter/bedding. Avoid clay litter because it can be toxic to rabbits. Cedar shavings, corncob and walnut shells are also not recommended for rabbits.
A rabbit often has a preference for a specific spot to defecate, such as a corner of its cage/pen. Watch your rabbit to see where it prefers to go, and put a litter box there. If your rabbit uses more than one spot, use more than one litter box.
Entice your bunny to use the litter box by placing hay or a treat in it. If your rabbit ignores the litter box (i.e. drops fecal pellets outside the litter box) gather up the stray pellets, and put them all in the litter box.
NOTE: After about two weeks of consistent “reminding” of where the droppings go, my bunny finally got the point.
Once your rabbit is reliably using a litter box, remove the other boxes until only one or two are left. Once you’ve conquered litter box training in your rabbit’s cage or pen, apply the same principles for litter training in its exercise area. Start with a small area (corner off a small part of a room), and later increase the size.