Mass protests in Cairo's central Tahrir Square pressured Hosni Mubarak to resign as president in 2011. Egyptians, in their first-ever democratic election, chose Mohamed Morsi, a candidate from the Muslim Brotherhood's Freedom and Justice Party, as their next president the following year.
Kerry said Wednesday, however, the spirit of the revolution "got stolen by the one single-most organized entity in the state, which was the [Muslim] Brotherhood."
Morsi was criticized for emphasizing the Islamic ideology of the Muslim Brotherhood during his brief tenure. He was removed from power by the military in July following months of civil unrest.
Western assistance to Egypt was curtailed when the military was accused of using force to quiet its opponents.
Kerry said many of the revolutions in the Middle East and North Africa were started because the nation's youth were hungry for a chance at success.
"Those kids in Tahrir Square, they were not motivated by any religion or ideology," he said.
There was no comment Thursday from the Muslim Brotherhood on Kerry's comments.
Kerry was addressing the 28th annual briefing of the Overseas Security Advisory Council, a federal council established to harmonize interests between the private sector and the U.S. State Department, in Washington.