He raised the alarm at 8.50am on Thursday and Stornoway Coastguard put out a Mayday relay asking vessels in the area for help.
Caledonian MacBrayne’s MV Lord of the Isles ferry responded and made a slight detour from its route to pick up the man between Skye and Canna.
He was taken on board and was said to be safe and well. His boat later sank.
Mallaig RNLI lifeboat was also sent to the scene but the ferry reached the fishing boat first.