The shed had been operating at the school for six months.
"I just loved the idea," Mr Pepper said.
"We raised some money to put a shed on the site, and it was working well."
Uplifting the shed would've been a challenge according to Mr Pepper.
"It was bolted down, and it weighs about 300, maybe 400kg. It would've taken a few people."
The school intends to keep the "sharing" scheme going even if they can't find their missing shed.
"We would love to keep it going, and we'd love to have money for another one, if that means more bake sales then we're not going to stop."
A similar uprooting was recently made at Motu Moana Scout Camp, five minutes drive from St Dominic's School.
The shed that was stolen housed giant chess pieces, which were also taken.