Kerry, 71, was flown by helicopter to the Geneva university hospital (HUG) following the accident in Scionzier, France, near Chamonix in the French Alps.
His spokesman said Kerry broke his leg and was in "stable condition".
After a night in the Geneva hospital Kerry was set to return to the United States for treatment.
"The secretary is stable and never lost consciousness, his injury is not life-threatening, and he is expected to make a full recovery," spokesman John Kirby said.
The accident occurred at around 9:40am, the statement said.
Kerry decided to cycle a route that had been part of the Tour de France on Sunday morning using a bike that he had brought with him.
French officials said that Mr. Kerry had coordinated the cycling trip with the local authorities.
Kerry fell as he was riding at a low speed at the start of a challenging climb up the Col de la Colombière.
"Paramedics and a physician were on the scene with the secretary's motorcade at the time of the accident," an earlier statement said.
Kerry held talks Saturday in Geneva with his Iranian counterpart Mohammad Javad Zarif in efforts to secure a nuclear deal ahead of a June 30th deadline.
The talks did not go into a second day as planned after Tehran rejected a key Western demand for site inspections.
Spokesman Kirby said that Kerry broke his right femur.
“Given the injury is near the site of his prior hip surgery, he will return to Boston (on Monday) to seek treatment at Massachusetts General Hospital with his doctor who did the prior surgery,” he said in a statement.
Kerry was reportedly in good spirits and expected to make a full recovery.
The accident has forced him top cancel meetings on Monday in Spain and on Tuesday in Paris, where a meeting of ministers from countries aligned against Isis (Islamic State) is scheduled.
Kerry is expected to participate in the Paris meeting by video conference.