Aberdeen Shaughnessy signed for
Aberdeen in June 2009, having previously played for Irish club
Salthill Devon as a youngster. Shaughnessy made his debut on 14 May 2011 against
Hibernian. A few days before making his debut, he signed a contract extension on a two-year deal. On 30 August 2011, Shaughnessy went on loan to
Forfar Athletic until January, along with
Nicky Low. Shaughnessy made his debut for the club on 11 September 2011 in a 1–0 win against
Brechin City. He then scored his first goal for the club, in a 4–2 win over
Stirling Albion on 17 September 2011. Shaughnessy would score twice in two games; in a 4–3 loss against
East Fife on 1 October 2011 and another in a 1–1 draw against
Arbroath on 15 October 2011. Ahead of the
fourth round of the Scottish Cup, a tie against his parent club, manager
Dick Campbell says he wouldn't put Shaughnessy and Low in the match against his parent club. Aberdeen won 4–0 and progressed to the next round. After impressing on loan, he went back to Forfar until the end of the 2011–12 season. He went on to make 26 appearances and scored three times. in 2012Ahead of the 2012–13 season, manager
Craig Brown believed Shaughnessy and Low had performed well at Forfar Athletic and considered him using them in the first team in the near future. In pre-season friendly matches, Shaughnessy scored twice in a 12–0 win over VfB Alstatte and a 2–1 win over
Manchester United as part of
Neil Simpson testimonial on 14 August 2012. On 7 December 2012, Shaughnessy signed a contract extension with Aberdeen until 2015. He scored his first competitive goal for Aberdeen four days later in the
Scottish Cup Fourth Round Replay win over
Motherwell. In the 2013–14 season, Shaughnessy played in the right-back position at the start of the season. Shaughnessy was even compared to
Richard Gough, due to his playing style. Shaughnessy scored his first goal of the season, in the
third round of the Scottish League Cup, in a 5–0 win over
Falkirk. He then received a red card in a 2–0 win over
Motherwell on 30 October 2013. It was his first red card of his professional career and this resulted in him missing some matches. Shaughnessy subsequently had his first team opportunities limited, as
Shaleum Logan or
Ryan Jack were preferred in the right-back position. Shaughnessy did not start a game for Aberdeen in the early part of the 2014–15 season and was loaned out to
Falkirk. He made his debut on 6 September 2014, as Falkirk lost 1–0 against
Stranraer in the
Scottish Challenge Cup. After making nine appearances for the club, it was announced that Shaughnessy would return to his parent club on 3 January 2015. Following his return, Shaughnessy made two more appearances, including making his first start, in a 1–0 loss against
St Johnstone in the last game of the season. On 14 May 2015, Shaughnessy was named as one of seven players who would be leaving Aberdeen at the end of the season, having not been offered a new contract.
St Johnstone Shaughnessy signed a pre-contract agreement with
St Johnstone on 20 May 2015, agreeing a two-year deal. In October 2017, he was named as St Johnstone captain, replacing
Steven Anderson in the role. He left St Johnstone at the end of the 2018–19 season.
Southend United After a trial spell with Southend United, he subsequently signed a one-year deal with the Shrimpers on 1 August 2019. He made 21 appearances during one season with the club, which triggered an extension to his contract, but he was released by Southend on 2 July 2020.
St. Mirren On 20 July 2020, Shaughnessy signed a two-year deal with
St. Mirren. He was named vice-captain in October, before becoming the captain in January following the departure of Sam Foley. On 21 May 2021 Shaughnessy signed a contract extension with the club lasting until 2023. He was named as
club captain by manager
Tony Docherty in July. He would make his competitive debut in an away
Scottish League Cup group stage win against
Bonnyrigg Rose. Shaughnessy scored his first two goals for the club in quick succession on 28 October as he netted a late brace to clinch a win away to
Livingston. It would not be his last time being the late hero for the
Dee, with December seeing both a last-minute goal against
Ross County to snatch all three points, and an equaliser away to
Kilmarnock which salvaged a point. Having played in every minute of Dundee's impressive season in which they had achieved top six, Shaughnessy would suffer a "significant" knee injury early into a league draw at home to
Rangers in mid-April 2024, which was confirmed a few days later to have ended his season following the announcement that the injury was a
ruptured ACL. As his injury was significant enough to rule him out for at least half of the following season, Shaughnessy began working more with the coaching staff. After making his return to the pitch in a
reserve league match away to
Kilmarnock, Shaughnessy returned to Dundee's named squad on 5 February 2025, as an unused substitute in the league away to
Celtic. Three days later, Shaughnessy made his first competitive appearance for Dundee since April 2024 as a substitute in a
Scottish Cup fifth round victory over
Airdrieonians. On 7 March, a now regularly-starting Shaughnessy scored his first goal back from injury in a
Scottish Cup match away to
Heart of Midlothian. On 17 June 2025, Dundee announced that Shaughnessy had departed the club.
Newcastle Jets On 9 July 2025, Shaughnessy signed a two-year deal with the
Newcastle Jets in the
A-League. On 4 October 2025, the Jets won the
Australia Cup against
Heidelberg United. Shaughnessy won the
A-League Men Premier Plate in 2026 with Newcastle after topping the table. ==International career==