The body of Saied Ali Eldin has been taken by hearse from the pier at Union Hall to Cork University Hospital.
Mr Eldin's body is the final body to be recovered after the Tit Bonhomme sank over three weeks ago.
His body was brought ashore just before 2pm to a temporary mortuary on the quayside where he was formally identified by his father, Mohamad.
After Muslim and Christian prayers, his coffin was slowly taken from the quayside in a hearse followed by his family, members of the Egyptian community, and many local people.
Although the search operation was scaled down on Sunday, foreshore and sea searches have been continuing.
Valentia Coast Guard says the body was spotted from a vessel involved in the sea search just before 1pm.
The body of the skipper of the Tit Bonhomme, Michael Hayes, was recovered at low tide on Wednesday.
His funeral will take place in Ring in Co Waterford at midday tomorrow.
The Tit Bonhomme sank in heavy seas early on Sunday 15 January.
Five men lost their lives in the tragedy when the trawler sank.
The bodies of crewmen Kevin Kershaw, Attia Shaban and Wael Mohammed were recovered in the days following the sinking.