He was flown to Geneva University Hospital by helicopter after the accident near Scionzier, about 40km (25 miles) from the Swiss border.
Mr Kerry has called off the remainder of his four-nation trip and will remain in hospital overnight.
"Secretary Kerry broke his right femur in a bicycling accident this morning in Scionzier, France," State Department spokesman John Kirby says.
"Given the injury is near the site of his prior hip surgery, he will return to Boston today to seek treatment at Massachusetts General Hospital with his doctor who did the prior surgery. The Secretary is stable and never lost consciousness, his injury is not life-threatening, and he is expected to make a full recovery," he said.
Kirby added that Kerry was in "good spirits and grateful to the French and Swiss authorities, doctors, and nurses who assisted him after the accident."
Kerry fell after hitting a curb while cycling part of the Tour de France route near the town of Scionzier, France, southeast of the Swiss border. He was airlifted to a hospital in Geneva.
It's unclear whether Kerry needs surgery, or how a lengthy rehabilitation might affect nuclear talks with Iran. Kerry has been the lead negotiator in several sessions with Iran over the past two years.
He had been in Geneva for a Saturday meeting with Iranian Foreign Minister Mohammad Javad Zarif.
The sides in the negotiations have been working toward a June 30 deadline for a comprehensive nuclear accord between Iran, the U.S., France, Britain, Germany, Russia and China.
Kirby said Kerry will participate remotely in this week's conference in Paris on the Islamic State threat.
Kerry, 71, is an avid cyclist and often brings his bike on diplomatic missions. He took bike trips during breaks in talks earlier this year with Iran and the other nations.
