Purchase the right boxes
Bunnies like to have enough room to stretch out in their boxes and, if you have a bonded pair, you have to allow enough room for both of them. We recommend medium to large size litterboxes (not the deep or covered varieties). Your bunny will probably appreciate - and insist on - having more than one litter location.
Get the right litter
There are several important litter dos and don'ts when it comes to bunnies:
Yesterday's News, recycled newspaper pellet litter / animal bedding
Carefresh (or similar) paper pulp litter / animal bedding
Wood stove pellets (these are used as fuel for woodstoves, but are actually great as bunny litter pellets.)
Ground corncob pet litter / bedding
Always check the label. Don't buy litter that cedar, cedar oils, zinc or the clumping clay.
Do NOT choose:
Clay litter! This can cause serious respiratory problems.
Cat Works litter! This can cause zinc poisoning and death.
Pine or Cedar litters! These can also kill your rabbit.
Fill the litter box properly
If you've had a bunny before, you know that you can do nothing right...especially not the first time. So, it might take some trial and error to find the 'proper way' to fill the litter box (according to your bunny, that is).
Start with around one inch of litter.
Prepare to do a little clean-up
Nobody's perfect. Your bunny will probably have a few accidents as he or she is learning to use the box.
Always remember: rabbits do not respond well to physical discipline. They have been designed to be easily frightened and broken; never physically discipline your rabbit. You and/or your rabbit could end up seriously hurt and your rabbit will end up terrified of you rather than your loving companion.
Use products like Nature's Miracle or Urine Off Small Animal Odor & Stain Remover to clean up those accidents.
How to litter train your bunny
1. Choose your location
While you are litter training your bunny, he or she will have to stay in an enclosed area. So, before you start training, choose and prepare the training area. A bathroom, utility room, or other small room without carpeting is a good place to start the training. You can also use a cage or an x-pen.
If you are training in a room with slippery floors, put a rug or towel down for the bunny to lay on.
Trim your bunny's nails. This will help him or her feel more comfortable on a slippery floor.
Be prepared to confine your bunny for a while. You can't let him out into any other room until he is always urinating in his box.
2. Prepare the litter box
Use 1" of litter. Add in some of the rabbit's poops and urine-soaked paper or hay. Place the litter box wherever the bunny seems to prefer to use, which is often a corner.
3. Add bunny
When you first let her into the training area, stay in the room. When she leaves droppings on the floor, immediately put both bunny and the droppings in the litter box. Tell her what a good bunny she is and pet her. Spend as much time as you can with her and when you have to leave, put her back into her cage or enclosure. A baby gate (not light plastic) works well to divide a room into a manageable space. Repeat this often until she has the training room mastered. Only then can you let her out into another room. Clean up accidents ASAP.
If the rabbit likes to dig and moves the box around, you can use a large metal clamp to fix it to the side of the hutch. You might also drill a small hole in the side of the box and secure it with twist ties.
Let the litter box stay a little dirty while the rabbit is learning. If you keep it too clean she will think that she is not supposed to use it.
4. Expand the area
After you are sure that your bunny is urinating only in the box, it's time to expand her area. Repeat step three in additional rooms.
Don't be afraid to use multiple litter boxes until your rabbit exhibits the appropriate litter box behaviors. Be sure and clean up behind any "accidents." If you witness your rabbit urinating outside their litter box, pick your rabbit up and place them in their litter box. Don't scold your rabbit, rather praise him/her once inside the litter box.
You can set a schedule while your rabbit is enjoying out time. Every 10 minutes place your rabbit in their litter box and praise them. Have a treat ready and offer it if they actually use the litter box. As time progresses, you can space out the amount of time between the reminder visits to their litter box. Time, patience, praise and consistent work will help your rabbit reshape their behavior.
Article Credit: http://rabbithaven.org/litter-training/