The U.N. says 9,000 people have died in Syria since the uprising began in March 2011.
Ford, who left Syria as security conditions worsened, will be in Boston to accept the award. The Denver native, who now lives in Baltimore, remains the U.S. envoy to Syria.
"He's exactly the kind of American that we want to celebrate and be proud of who's engaged in building a more just and peaceful world," Kennedy said. "We need more courageous public servants in all areas of our government and he's certainly one of those and will, hopefully, show a path to others to follow his example."
Last year's award went to Wael Ghonim, the Google executive credited with helping to inspire the uprising in Egypt.
The Profile in Courage Award is named after the JFK book "Profiles in Courage," winner of a Pulitzer Prize in 1957.
Past recipients include President Gerald Ford and former U.N. Secretary General Kofi Annan, who is now a U.N. special envoy working on a tenuous peace plan for Syria.
This year's award also celebrates what would have been the late president's 95th birthday, on May 29.
"Hard to imagine, but it means a lot to our family that 50 years after his death, people still care about his vision and his ideals and so it is a wonderful thing to be able to celebrate people who are carrying ideals forward in today's world," Kennedy said. "And that's what Profile in Courage Award is all about."