Fitzpatrick came through the youth system at Motherwell and made his debut against Celtic on 12 May 2004.
In 2004–05, Fitzpatrick scored a last-minute winner in a Scottish League Cup semi-final against Hearts at Easter Road. The 3–2 win after extra time earned Motherwell their first major final appearance since the 1991 Scottish Cup Final. Remarkably, it was his first senior goal for the club. In May 2008, Fitzpatrick signed a two-year contract extension with the Fir Park outfit.
On 13 January 2011, Fitzpatrick signed a two-year deal with Ross County, after rejecting the offer of a six-month extension at Fir Park.
Fitzpatrick joined the Dumfries club, Queen of the South on 19 March 2013, until the end of the season.
Fitzpatrick moved to Greenock Morton on 9 July 2013, after playing in a trial match against former club Motherwell on the Saturday. He left the club at the end of the season in search of part-time football.
On 4 June 2014, Fitzpatrick signed for Airdrieonians.