The shop near the isle's pier was left open to visitors so they could use its wi-fi and replenish supplies, leaving the money in an honesty box.
But when volunteers checked the shop over the weekend they found sweets, toiletries, batteries and six hand-knitted hats had been stolen.
On Facebook, Isle of Canna Community Development Trust said it was "gutted".
The trust has started locking the shop when it is not staffed.
Police Scotland wants to speak to anyone who docked at the pier on Friday night.
The National Trust for Scotland, which owns the island, said: "We were sorry to hear about this theft from the shop on Canna, which the community have worked hard to make a success.
"Thankfully, incidents like this are extremely rare and Canna is a very safe place."
Canna is the most westerly of an island group called the Small Isles.
The community shop on Canna has been robbed in what is thought to be the tiny island's first crime for decades.