Kirk said taking over the Massachusetts seat left him with mixed emotions, particularly because he was still feeling the "profound absence" of his old pal.
"It's exhilarating and sobering at the same time," Kirk said.
Democrats applauded his arrival. Kirk's swearing in by Vice President Joe Biden gave Senate Democrats a filibuster-resistant, 60-vote majority with the health care fight at a critical juncture. Contentious battles also lay ahead on climate change and financial regulation.
The swearing in came just a few hours after a Massachusetts judge rejected a Republican request to delay it.
The state GOP had argued that Democratic Gov. Deval Patrick exceeded his constitutional authority by appointing Kirk before a traditional 90-day legislative waiting period had expired. State lawmakers passed a bill this week giving Patrick the power to choose an interim senator.
Kirk said he did not spend much time worrying about the GOP's legal challenge.
"We're prepared to go to work," he said.
The Boston attorney, 71, will serve in the interim post until Massachusetts voters pick a replacement in a Jan. 19 special election.
"It's the highest honor in my life, accepted in humility," said Kirk, who became the sixth appointed senator this session.
He has pledged not to be a candidate in the special election.
Kirk, a fixture in national Democratic circles for decades, was on Kennedy's senatorial staff for eight years and served as chairman of the John F. Kennedy Library Foundation.
He is a veteran Washington insider, who has ties to many of the capital's most powerful figures in politics and government.
Kirk was one of Kennedy's most trusted aides, a point underscored when Kennedy made Kirk executor of his will. Kirk was master of ceremonies for a memorial service the evening before Kennedy's funeral.
Kennedy's widow, Victoria Reggie Kennedy, his daughter, Kara Kennedy Allen, and his sons, Edward Kennedy Jr. and Rep. Patrick Kennedy, D-R.I., were on hand for the swearing in.
Before the ceremony, Kirk visited the graves of Kennedy and his two slain brothers, President John F. Kennedy and Sen. Robert Kennedy, at Arlington National Cemetery.
Kirk also met with Kennedy staffers, who broke into applause as he arrived at their office. He has asked Kennedy's staff to remain onboard.
Kennedy died Aug. 25 after a yearlong battle with brain cancer.