Manager Kenny Shiels allowed Clancy to leave the club in order to rebalance his defensive options, with Ryan O'Leary out injured.

[15] On 28 February 2014, Clancy signed for St Johnstone on a contract until the end of the 2013–14 season despite interests from Derry City.

Despite having one of the lowest budgets in the league, Clancy led the club to impressive victories against St Patrick's Athletic, Derry City and rivals Dundalk.

Clancy had to deal with the losses of Robbie Benson, John Mountney and Sam Bone who followed former head coach Stephen O'Donnell to Dundalk, while also losing other key players such as Lee Desmond, Alfie Lewis, Matty Smith and Vítězslav Jaroš.

In terms of incomings, Clancy signed Joe Redmond, Mark Doyle and David Odumosu who he had worked with previously at Drogheda United, along with former Hibernian teammate Eoin Doyle and Joseph Anang, Jack Scott, Tom Grivosti, Anthony Breslin, Tunde Owolabi and Adam O'Reilly.

[24] His first taste of managing in European football was in Pat's UEFA Europa Conference League campaign, which started out with a 1–1 draw at home to Slovenian side NŠ Mura.

[26] The next round saw Pat's beat Bulgarian side CSKA Sofia 1–0 away[27] before suffering the heartache of a 2–0 loss in the second leg following a controversial late penalty.

[28] Clancy's side finished in 4th place at the end of his first season in charge, securing UEFA Europa Conference League football for 2023.

[29] Clancy was awarded his UEFA Pro Licence in December 2022, the highest coaching qualification in world football.

[30][31] On 2 May 2023, Clancy departed St Patrick's Athletic by mutual consent with the club in 7th place, 13 games into the 2023 season.

[32][33] On 24 November 2023, Clancy was announced as the new manager of Cork City, who had recently been relegated to the League of Ireland First Division.