"Richard Chassiot, who had been president of Swiss Cycling since March 2012, has resigned with immediate effect," the federation said on its website.
"He has left the Swiss cycling federation over disagreements within the executive committee on the nomination of Pat McQuaid," the statement added.
This week's decision not to support McQuaid ended a long debate within the Swiss federation over whether to back the Irishman. A commission had been set up to discuss the case, only to be dismantled after the national body decided to step back.
McQuaid, who failed to get support from his own federation to run for a third term as International Cycling Union (UCI) president in next month's election, still has the backing of the Thailand and Morocco governing bodies.
He has been widely criticised over the Lance Armstrong doping scandal amid allegations the UCI did not do enough to catch the American, who was stripped of his seven Tour de France titles last year.
Brian Cookson, head of British Cycling, has based his candidacy on restoring trust and credibility in the sport but McQuaid has described his rival's manifesto as "half-baked, fundamentally flawed and financially impractical".