The 30-year old Scot started off his career at Celtic as a trainee, during which time he spent a half-season loan at then Championship side Sheffield United in the opening part of the 2002-03 campaign, McGovern making 14 starts, two substitute appearances and scoring three goals for the Blades. The Glasgow-born midfielder then moved away from Parkhead, after not making any first-team appearances in a hooped shirt, on a permanent basis when he joined then Scottish Premier League outfit Livingston on a free transfer in July 2003, McGovern going on to make 12 starts and play 20 times from the bench in a goalless spell with the Almondvale club.
Former Owls boss Paul Sturrock then took Jon-Paul to Hillsborough in the summer of 2004 as McGovern signed a two-year deal with Sheffield Wednesday, the winger making 57 starts, four substitute appearances and scoring eight goals in what would become an injury-hit spell in South Yorkshire. At the end of the 2005-06 campaign the Glaswegian was released by the Owls and he subsequently moved to MK Dons in pre-season 2006 where he spent just over one year while making 51 starts, seven substitute appearances and scoring four goals for the Buckinghamshire side.
Paul Sturrock wanted McGovern back though and so he signed the winger for Swindon on a three-year contract for an undisclosed fee from MK Dons, just two hours before the August 2007 transfer deadline. The 30-year old had a successful time with the Robins in his first two and a half years and so signed a two-year contract extension in January 2010 to tie him to the Wiltshire club to the end of June 2012. McGovern, up to the end of last season, having made 157 starts, 20 substitute appearances and scored 12 goals in his four years with Town.
That deal to the summer of 2012 has been paid up the Robins though as they look to get their high earners off the wage bill following their relegation to League Two last season. McGovern, along with fellow recent signing Andy Welsh coming into the the Carlisle squad from the 1st of July on a two-year contract to the end of June 2013 to offer some width for the Cumbrians, although where that leaves the diamond formation is open to question unless the pair are destined to begin their Blues careers as benchwarmers.