Kerry broke his femur but the injury is not life-threatening and he is expected to make a full recovery, spokesman John Kirby said. He was taken to Geneva's main hospital and was in a stable condition.
He has canceled visits to Madrid and Paris.
Kerry had been due later on Sunday to travel to Madrid, his first visit to Spain as secretary of state, to sign a bilateral defense agreement that would allow the United States to have permanent use of Moron air base, near Seville.
He had then been due on Monday to fly to Paris for a meeting with Iraqi Prime Minister Haidar al-Abadi and members of a U.S-supported coalition fighting the militant group Islamic State.
Kerry, 71, is still an avid sportsman and often takes his own bike on official trips abroad. The accident came the day after he met his Iranian counterpart Mohammad Javad Zarif in Geneva to try to overcome obstacles in negotiations on curbing Tehran's nuclear program.
It was not immediately clear how his injury would affect the nuclear negotiations with just a month left before a June 30 deadline for a final agreement between Iran and the United States, Britain, France, Germany, Russia and China.
Kerry was flown by helicopter from the scene of the accident after he was stabilized by a doctor and paramedic who were with his accompanying motorcade. He was resting comfortably and in good spirits in the Geneva hospital, Kirby said.
A senior State Department official said it appeared Kerry had hit a curb. There was no vehicle involved.
Kerry was to return to his home town of Boston on Sunday for treatment at Massachusetts General Hospital. His plane and traveling party were departing France ahead of Kerry, who was to take another plane outfitted to ensure his comfort as a precaution, Kirby said.
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