The crew of the Ardglass-registered boat, the Snowdonia, were rescued by another trawler.
A lifeboat from Kilkeel assisted in the effort to help the men.
A spokesman from the RNLI said the Dublin coastguard helicopter had taken the men to Daisy Hill Hospital. They were later discharged.
Belfast Coastguard said it received a call from the fishing vessel, Tribute, to inform them they had recovered two fishermen from the water.
The crew of Kilkeel Inshore Lifeboat provided first aid until the rescue helicopter arrived.
Gary Young, Watch Manager Belfast Coastguard, said: "This incident has again proved the importance of wearing a life jacket and having it maintained to a high standard.
"I would like to pass on my thanks to the professionalism of the lifeboat and helicopter crews."