 Flannery was the first player to score at the new Strathclyde Homes Stadium in a competitive fixture, netting in 3–0 win over Elgin City back in December 2000.In November 2012, he signed for junior side Rutherglen Glencairn.On 2 May 2014, Paddy Flannery and John Doyle become co-managers at Cambuslang Rangers.