The alarm was raised at about 6.30am Saturday when a commercial fishing vessel found a 45-year-old man signalling for help in the water off the coast of Townsville.
He and a mate had been fishing in a small tinny when the men fell out of the boat into the water off Sandfly Creek.
The current dragged their boat away quicker than they could swim after it.
The pair attempted to swim back to shore but lost contact with each other during the night.
The 45-year-old man was rescued by the commercial ship in Cleveland Bay off Townsville and taken to shore where he was treated for exposure.
He was taken to hospital in a stable condition, but a 41-year-old Townsville man is still missing.
Police have launched a large-scale search for the fisherman and the missing boat.
Three helicopters and nine boats are involved in the search across a wide area.
It's unknown exactly where the men fell into the water or where the missing man may have ended up.
"We unfortunately don't have a starting point or reference point in relation to where the boat was," Qld Police acting senior sergeant Jayson Cooke said.
"The gentleman (rescued on Saturday morning) was in the ocean for up to six hours, so it is a blanket search of the area at the moment."
Anyone who spots the four-metre, white Quintrex coast runner Queensland registration RD806Q is urged to contact police.
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