The solemn scene was played out under the watchful eyes of Kennedy's extended family and friends, who then followed the flag-draped coffin inside.
The police-led motorcade that had transported Kennedy's body on a circuitous route from Hyannis, Mass., was greeted by thousands of people, many applauding, as it made its way to Boston. The 65-mile trip took nearly three hours.
Admirers of the late liberal Democratic senator lined the roadway and streets -- several deep at some points -- with some displaying U.S. flags and waving to the passing hearse and motorcade, CNN reported. At least one weeping woman said she arrived hours earlier to pay her last respects.
The motorcade took a meandering route, passing several historic sites that had particular meaning to the senator and his family.
U.S. President Barack Obama will eulogize Kennedy at his funeral in Boston, Kennedy's office said. Former Presidents George H.W. Bush, George W. Bush, Jimmy Carter and Bill Clinton also will attend, CNN said.
Kennedy, who represented Massachusetts in the Senate for nearly 50 years, died at his home in Hyannis Tuesday after a long bout with brain cancer. He was 77.
Kennedy's funeral will be Saturday morning at Our Lady of Perpetual Help Basilica in Boston's Mission Hill area, CNN reported.
Kennedy will be buried near brothers John and Robert in Arlington National Cemetery near Washington later Saturday afternoon, his office and the Defense Department said.
Before the funeral, Kennedy's body will lie in repose Thursday and Friday in the Smith Center at the John F. Kennedy Presidential Library and Museum in Boston, CNN said. A memorial service will be Friday at the Smith Center.
Kennedy is eligible for burial at Arlington because of his congressional service and his military service in the U.S. Army from 1951-53. The proposed grave site is 95 feet south of the grave of Sen. Robert
Kennedy, the Pentagon said. Robert Kennedy's grave is a few feet away from the grave of their brother, President John F. Kennedy.