Flannigan started his career at Kilmarnock and debuted on 25 September 2007, as a first-half substitute in a 2–0 defeat to Hamilton Academical in the third round of the Scottish League Cup.
On 6 October 2007, Flannigan's Scottish Premier League debut was as a 19 year old in a 2–2 draw versus Inverness Caledonian Thistle.
[1] On 22 March 2008, Flannigan scored his first goal for the club in a 4–1 home victory versus Inverness Caledonian Thistle.
[4] In March 2012, Flannigan went on trial with Greenock Morton and debuted in a draw versus Ross County.
[6] During this period Flannigan sustained an elbow injury that required surgery and he departed the club at the end of his contract.