In Parliament Alistair Burt became the Parliamentary Private Secretary (PPS) to the Secretary of State for the Environment Kenneth Baker in 1985, he remained as PPS to Baker in his role as Secretary of State for Education and Science from 1986 and in his role as the Chancellor of the Duchy of Lancaster from 1989 until 1990. After the 1992 General Election Burt was promoted to the government of John Major and became the Parliamentary Under Secretary of State at the Department of Social Security where he remained until 1995 when he was promoted further with the rank of Minister of State at the same department. He was one of many ministers who lost their seats at the 1997 General Election when Bury North fell to Labour's David Chaytor by 7,866 votes.
Alistair Burt re-entered parliament at the 2001 General Election for the very safe Conservative seat of Bedfordshire North East which had been represented in parliament by the former Attorney General Nicholas Lyell who had retired. Burt was re-elected comfortably with a majority of 8,577, and has remained as an MP since. He was made an opposition spokesman on Education and Skills under William Hague in 2001, before he became the PPS to the Leader of the Opposition Iain Duncan Smith in 2002 and carried on as PPS to the new leader Michael Howard. After the 2005 General Election he rejoined the front bench and is a spokesman on Local Government Affairs and Communities. However in January 2008, Burt was promoted to Assistant Chief Whip and Deputy Chairman of the Conservative Party with responsibility for Internal Development.