He was one of five crew on board when a large wave hit the vessel about 25 miles south east of Newcastle.
An Irish coastguard rescue helicopter 116 was called out from Dublin during the early hours of Tuesday.
The man was airlifted to Daisy Hill Hospital in Newry where he is being treated for head and chest injuries.
He is in a stable condition.
An injured man has been airlifted to hospital after he fell from his fishing boat in rough seas near the coast in County Down.