Kitten thin and losing hair

I have a pair of orphaned kittens that I rescued back in early November at about 3 weeks old. They are now about 3 months. One of the kittens is perfectly fat, fluffy, and happy, but his brother for some reason hasn't been putting on weight and his hair is thinning. The one that is healthier was originally the runt and the other was the largest of the litter(were 3 originally. Other found a new home) But now the runt is larger. They are fed free choice and are kept indoors. I'm at a loss as to what could be since it is affecting one kitten but not the other. Anyone have any ideas what it would be?

Some kittens just fail to thrive. I'd recommend putting the skinny cat on a wet food only diet and feed him 2-3 times a day. No harm in adding his brother to this diet too. Dry free feeding can cause UTIs and other health problems. It seems like the sick kitten just isn't eating much so you should buy yummy flavored wet food and supervise to MAKE SURE he eats.

I really hope he will do better soon! Are these indoor only cats?

Has he been checked for fleas? That could be causing the hair loss. Oh, and I wouldn't worry about his weight unless he was terribly thin, because some cats just ARE thin. I have a black cat who wasn't even the runt of her litter and as well as being tiny, she's very thin and delicate. I've tried fattening her up with all sorts of treats but have come to accept that she's just skinny. The vet says she's the healthiest of all of my cats so yeah.

I agree with Silmarien, about wet food only and supervising him while he's eating. You could try crushing treats to sprinkle over the wet food to tempt him, too - works every time with my cats. ^_^