The man's colleague raised the alarm after he fell from the vessel in the Summer Isles near Ullapool at around 10.30am yesterday.
The colleague managed to pull the man from the water back on to the boat.
He was then flown to Western Isles Hospital in Stornoway by coastguard helicopter Rescue 100.
Police Scotland said that the man had died.
The Marine Accident Investigation Branch will investigate the incident, along with police and the coastguard.
The fishing boat was a local vessel from Loch Ewe.