In the 1999 election ACT ranked her tenth on its party list, and she narrowly missed out on a seat in Parliament. In the 2002 election, however, ranked ninth, she won election as a list MP. She also contested the United Future safe seat of Ohariu-Belmont, polling fifth.

In June 2005, she won promotion from ninth list position to second – even before she became the party’s deputy leader. In the 2005 election, she again campaigned for ACT party vote and accompanied Rodney Hide through much of his Epsom campaign. However, she also stood in Ohariu-Belmont, coming fifth.

In 2006, she completed basic and corps training as a Reserve Forces field engineer (Royal New Zealand Engineers) within the New Zealand Army. Whilst Associate Defence Minister, she was required to transfer to the non-active Reserve but, since leaving the Executive Council has resumed active training.

In the 2008 election, she contested the electorate of Wellington Central, a seat formerly held by former ACT leader and co-founder Richard Prebble from 1996 to 1999. Campaigning solely for party vote, she polled fourth in the electorate count but was re-elected to Parliament on the ACT party list.

In November 2008, as part of the Supply and Confidence Agreement between the ACT and National Party which allowed the formation of a Government, Heather Roy was appointed to ministerial posts outside the cabinet as Minister of Consumer Affairs, Associate Defence Minister and Associate Education Minister.

Following internal party concerns she was removed as deputy leader of the Act Party in August 2010. Her ministerial portfolios were transferred to the new deputy leader, John Boscawen, by the Governor-General following advice from the Prime Minister. Since 17 August 2010, she has assumed the roles of spokesperson on Foreign Affairs, Health, Social Development and Employment, Police, Corrections, Courts, Labour, Science and Innovation, Pacific Affairs, Ethnic Affairs, Arts, Culture and Heritage, Tourism, Sports and Recreation, Youth Affairs and Tertiary Education. She also sat on the Select Committees for Education and Science; Local Government and Environment as well as the Parliamentary Service Commission.

Roy also took charge of a bill submitted by Sir Roger Douglas, The Education (Freedom of Association) Amendment Bill (Voluntary Student Membership), which proposed to make membership of student associations and unions voluntary. The bill eventually passed its third reading in September 2011, and voluntary student membership is now required.

In June 2011, Roy announced her retirement at the 2011 general election.

Following the 2011 election, Roy was appointed non-executive Chair of the Board of the pharmaceutical lobby group, Medicines NZ.