McGowan started his career with Scottish Premier League club Celtic, but struggled to break into the first team and was sent out on loan several times.

During his spell at Cappielow, McGowan won the Scottish Football League's young player of the month award for January 2007.

[7] McGowan was loaned out to SPL side Hamilton Academical at the beginning of the January 2009 transfer window,[10] and started his first game with an assist for Chris Swailes in the 1–0 win over Ross County in the Scottish Cup.

He scored his first competitive goal for the Buddies in a Scottish League Cup match against Ross County – St Mirren lost in the penalty-shootout when the tie ended 2–2 after normal time and 3–3 after extra-time.

[19] In September 2010, McGowan received a straight red card for an off-the-ball violent incident involving Manuel Pascali of Kilmarnock, which was spotted by the referee.

After the match, McGowan apologised for his actions,[20] while his manager Danny Lennon stated a fine would be considered once video evidence had been reviewed.

In January 2011, McGowan scored the first hat-trick of his career in a 6–1 win over Peterhead in a fourth round replay in the Scottish Cup.

After scoring two goals at the outset of the 2012–13 season (in a 5–1 win over Ayr United in first round of the Scottish League Cup, and in a 3–1 loss against Kilmarnock on 22 September 2012), McGowan suffered a shoulder injury that required surgery.

[34] McGowan returned to the first team in mid-Decemberand went on to score a penalty against former employers Celtic in the Scottish League Cup semi-final; St Mirren qualified for the final with an unexpected 3–2 win.

[41] Eventually, on 3 June 2013, it was announced that McGowan had re-signed for St Mirren on a free transfer, just two days after his previous contract had expired.

[45] In the match against Inverness CT, McGowan limped off where he sustained a broken toe,[46] and later had to wear a protective mask in the fourth round replay of the Scottish Cup against Queen of the South.

[50] After the latter match, McGowan stated he was happy to put the disciplinary incident behind him by helping the club finish the season on a high.

[53] Upon joining Dundee, Manager Paul Hartley stated he immediately sought to signed him once he learned he was released by St Mirren.

[59] As a result of being placed on a court-imposed curfew for another incident outside football,[60] McGowan could not be included in the matchday squad for evening kick-offs for the remainder of the season, though he was still available for afternoon games.

[61] During a League Cup group stage match against Forfar Athletic in 2016, McGowan chipped Grant Adam on the edge of the box to open the scoring in a 7–0 win for Dundee.

He then scored in the opening league game of the 2016–17 season, a 3–1 win over Ross County in Dingwall, however afterwards Dundee would go into a six-game losing streak which saw the club involved in a relegation fight.

Towards the end of the season McGowan assisted Marcus Haber to score in a crucial match against Kilmarnock in a 1–0 win to help Dundee steer clear of relegation during Neil McCann's reign as interim manager.

[71] McGowan signed a one-year extension with Dundee near the end of June 2020, agreeing to drop his wages significantly for the year to help the club cope better with the coronavirus crisis.

[75] McGowan would mark his 300th appearance for the Dark Blues in September 2022, in what would be his first for the club outside of Scotland as Dundee defeated Welsh champions The New Saints away in the Scottish Challenge Cup.

[77][78] On 21 February 2023, McGowan reunited with former teammate and manager James McPake after joining Scottish League One club Dunfermline Athletic on loan until the end of the season.

[88] McGowan made his debut for the Galabankies in a win over Inverness Caledonian Thistle in the Scottish League Cup group stage.

[96] On 15 April 2015, McGowan was spared a jail sentence, but was placed on a restriction curfew for sixteen weeks and had to wear electronic tags, meaning he could not play in midweek matches for the duration of the order as he had to be at home by 7pm each day.

[60] Following the incident, McGowan apologised for his actions and said he hoped to become a better person, having a problematic lifestyle of alcohol and gambling,[97] while the club stood by him.

[99] In July 2018 McGowan was again convicted of assault, this time for spitting on a bouncer outside a Dundee nightclub two months earlier after attending the club's annual awards event; he again avoided a prison sentence for the offence and was instead given a community service order.