Four-year-old Poppy's hutch was smuggled out of Lamont City Farm, in Erskine, Renfrew-shire, during the raid.
Her custom-built 5ft by 5ft wooden pen is estimated to be worth more than £200.
The two thieves put Poppy – a continental giant rabbit – out of her home and made off with it, at around 7.30pm last Friday.
Trisha Craig, 29, who manages the animal welfare centre, said the cash-strapped charity can't afford to buy Poppy a new house.
She said: "I'm absolutely disgusted that someone would do something like this, especially to a charity - we're all so angry about what has happened.
"It's nearly Christmas and poor Poppy is now homeless, though at least they didn't hurt her."
Poppy has lived at the farm for three years but is now having to share a hutch with another rabbit.
Trisha said: "She's really not happy about sharing, there's just not enough room for her.
"Poppy is a big girl, which is why we had her in the bigger hutch.
"It's such a shame to see her unhappy."
The community farm, in the town's Barrhill Road, has been taking care of animals for 35 years. Its menagerie includesponies, sheep, birds and other rabbits.
Staff are also concerned after the same men were captured on CCTV taking pictures of one of the farm's rescue horses, Rio.
Trisha said: "We think they were looking to identify horses that they can steal then sell."
Police are probing the rabbit theft.
This is the second time in five months the community zoo has been targeted.
In August, the Evening Times told how a thief stole a baby python - by slipping it into his pocket.
Despite pleas from staff, King has never been returned.
After the 10-week-old snake was stolen, staff at the farm spent £500 on new locks.
But Trisha, added: "We can't afford to keep spending money on security and we rely on neighbours to keep an eye out for us."
Anyone with information on the thefts should call 0141 532 2000.