The accident happened early on Tuesday morning near Mannenbach in the canton of Thurgau.
Shortly before 7am Thurgau police were alerted that a crewless fishing boat was drifting on the lower of the two lakes that make up Lake Constance.
When the rescue services arrived they found the boy who had managed to swim to the shore.
The boy said he and his father had set out on a fishing trip and had fallen overboard.
Police boats and a helicopter of the air rescue service Rega began an immediate search for the missing man between Mannenbach and the island of Reichenau.
Divers were also called in to help in the search.
An investigation is underway into the cause of the accident.