Either his own space or with another one from his litter that doesn't pick on him(to reduce the stress from weaning and separation). Though in a couple of weeks all of them will need to be separated anyways before hormones kick in(unless they have already). And increase food, though if it were me I would be more inclined to free feed a grass hay instead of increasing pellets, though you do have to ensure that the rabbit is eating plenty of the hay.
Being a runt of the litter isn't always a genetic trait. It can be due to a correctable health problem. Ill thrift and wasting along the back and hindquarters can be an indication of parasites. I've had experience with two underweight kits, both had the appearance of being runts. One was a friends 5 week old bunny that wasn't gaining weight like it's siblings and just wasn't thriving. She suspected it might be due to worms and treated with a 10 day course of fenbendazole liquid wormer(20mg/kg), which is an antiparasitic used to treat the most common parasite in rabbits, the rabbit pinworm. Soon after treatment was started the kit began putting on weight normally and catching up with his siblings in size.
Another is a pet of mine. When she first came to me at 8 weeks old, it was thought she was a runt as she was at least half the size of her siblings. Later I noticed she was also quite skinny along the back and had a pot belly. She was on a pellet only diet prior to coming to me and I changed that to limited pellets and unlimited grass hay. In the weeks after changing her diet she lost her pot belly and started gaining weight normally. She caught up in size and weight and was no longer the runt. She is 4 now and is a normal weight and size for her breed, in fact she is at the larger end of the scale for her breed, so definitely not a runt. I didn't know at the time what the problem was, but now I'm better versed on rabbit health issues I suspect that she may have had hepatic coccidiosis, as the wasting along the back and a pot belly are often indications of it. Because I didn't know at the time she wasn't treated for that, but I can only assume that reducing her pellets(and thus available carbohydrates) and increasing her fiber through hay, is what corrected the problem(but this is only speculation on my part) as increased fiber/reduced carbs is often helpful in correcting some internal parasite problems. Though had I known at the time I would also have had her checked for cocci and treated with the appropriate meds.
So those would be the two possible causes and solutions that I would be looking at, worms and coccidiosis. As long as you've confirmed that the bunny just wasn't underweight because it wasn't fed enough food and water(if bun doesn't know how to drink or can't reach water bottle easily it won't drink enough, so won't eat enough).
You can get a fecal test done to verify if it is parasites, but be aware that sometimes the test isn't always accurate and thus treatment may be based on symptoms presented instead.
http://www.medirabbit.com/EN/GI_diseases/Parasitic_diseases/Nem_gen/Nematodes.htm
http://www.medirabbit.com/EN/GI_diseases/Protozoal_diseases/Cocc_en.htm
http://wildpro.twycrosszoo.org/S/00dis/Parasitic/Hepatic_coccidiosis_rabbits.htm
