Cantonal police said they were contacted on Wednesday at around 7.40pm about a man being in difficulty after falling off his board in an area of the lake near a water treatment plant in Lutry, east of Lausanne.
The man was already underwater by the time a rescue team arrived, police said.
The lake brigade of the Vaud gendarmerie, life-saving teams from the communities of Lutry and Pully and a Rega emergency rescue squad with a helicopter began searching for the victim.
The man's body was finally fished out of the lake by divers from the Vaud gendarmerie at 11.20pm, police said.
The victim, a resident of Brazil, was visiting a friend in Switzerland, police said.
Standup paddle boarding, a sport that originated in Hawaii as an offshoot of surfing, has become a popular activity in Lake Geneva, with numerous ports offering boards to rent.
The Brazilian was not known to be wearing a person flotation device (PFD), which is required for use with paddle boards in some jurisdictions.
The incident occurred as temperatures are beginning to soar above 30 degrees in many parts of Switzerland and people are flocking to beaches to cool off.
However, despite the warm weather, the water in Lake Geneva and other mountain lakes remains cool for swimming.
An investigation into the fatality is under way.