McGowan ran as an independent for the Division of Indi at the 2013 Australian federal election, against the Liberal incumbent Sophie Mirabella. The seat had long been believed to be a conservative stronghold; it had been held by a conservative party for all but nine years since Federation, and without interruption since 1931. However, a number of area residents felt Mirabella had taken them for granted. They formed a grassroots organisation, Voices for Indi, that eventually decided to draft an independent to run against Mirabella. After numerous prominent locals turned down the offer, McGowan finally accepted. After eleven days of counting, on 18 September, Mirabella conceded defeat and McGowan claimed victory, winning the seat with a final margin of 431 votes, a two-candidate preferred vote of 50.25 percent. Mirabella was the only Liberal incumbent to lose her seat at the 2013 election. The ABC's Barrie Cassidy described McGowan's candidacy as "a warning to the occupants of safe seats everywhere on both sides of politics." It was claimed in October 2014 that 20 McGowan supporters who formerly lived in Indi changed their electoral roll details back to Indi. The Commonwealth Department of Public Prosecutions pursued charges against two young voters. Their defence lawyers successfully argued the charges were "scurrilous" and that they had followed the Australian Electoral Commission's published advice in enrolling at their home address and on 5 April 2016 a Melbourne Magistrate dismissed all charges against the two voters and ordered the Crown to pay their court costs. Mirabella gained Liberal party preselection in late June 2015 to run for Indi in the 2016 federal election, However, McGowan retained Indi against Mirabella with an increased 54.8% two-candidate-preferred vote. Mirabella conceded to McGowan on 3 July 2016. Notably, the Liberal two-party-preferred vote in a "traditional" two-party contest against Labor was reduced to 54.4% against Labor's 45.6%, a marginal two-party result not seen since the 1929 election. McGowan has given the Coalition government confidence and supply support in the event of a hung parliament. In the lead up to the 2016 Federal election McGowan was present at a function in Wangaratta at the Benalla nursing home along with Sophie Mirabella. Both were candidates for the Division of Indi. It was subsequently reported on 20 April 2016 by journalist Libby Price in the Benalla Ensign that Mirabella had pushed McGowan at this meeting. McGowan was interviewed soon after the event and refused to confirm or deny the allegation. She was interviewed by The Border Mail and refused on four occasions to answer as to whether she had been pushed or not. The Benalla Ensign issued an apology on 26 October 2016 and stated that Mirabella did not push McGowan. Mirabella launched defamation proceedings against the Benalla Ensign and its editor Libby Price. The case was heard in the Victorian County Court in Wangaratta in early May 2018. McGowan was called as a witness in the case and gave evidence that Mirabella did not push her. The court found in favour of Mirabella that she had been defamed by the Benalla Ensign and its editor Libby Price. On 14 January 2019 McGowan announced she would not be recontesting Indi at the next election. On 18 May 2019, her preferred independent candidate, Helen Haines, claimed victory in federal election.
