Staff at Looking Glass Books in Simpson Loan, Edinburgh, say they were "sickened" by the crime.
The thief is understood to have made off with about £200 from the charity tub. The independent bookshop had raised the cash by wrapping books and other gifts in return for a small donation.
Shop owner Gillian Robertson, said it was heartbreaking that vulnerable children would miss out.
She said: "I was sickened when I first saw it had happened. We've had things stolen from the shop before by shoplifters, but to steal something that is meant for children living in refuges makes it even more sad."
Ms Robertson had counted the money, which she had earlier changed into notes to make it lighter. She was planning to take £500 to the charity after the weekend.
Police are investigating the theft and store bosses are to have CCTV installed.