The middle-aged man was spotted being pulled by the tide through narrow waters near Kylerhea at around 1pm on Monday.
Those on board the vessel made their way to rescue him and pulled him to safety.
Emergency crews were called to assist the man, who was suffering from hypothermia and exhaustion.
A Maritime and Coastguard Agency spokeswoman said: “He was very much feeling the effects of the cold, given that sort of temperature of water.
“It would appear that the fishing vessel had seen him coming through the narrows with the tide.
“They saw him capsize and went to help him.”
Kyle of Lochalsh RNLI’s volunteer crew arrived at 1.17pm and paramedics were already on the scene.
A Coastguard helicopter was called to airlift the casualty to Raigmore Hospital in Inverness.
It arrived on scene at 2.05pm and set off with the man winched on board at 2.20pm.