Duffy was born in Glasgow, growing up in the Maryhill area of the city (specifically the Wyndford estate) where he was a childhood friend and neighbour of Charlie Nicholas.
Duffy led First Division side Dundee to the Scottish League Cup Final in November 1995, but the team lost 2–0 to Aberdeen.
Going into administration meant that Dundee lost most of their talented players, but the team battled on and managed to avoid relegation that season.
[6] However, on 24 August 2005, the board then decided to sack Duffy after just four games of the new season, even though Dundee were top of the Scottish First Division.
[8] Duffy spent barely a month in that position, however, as he was dismissed by the club, along with manager Graham Rix, on 22 March 2006.
But after recording losses against Bristol City, Burnley and WBA he was not awarded the job on a full-time basis.
[17] At the start of the 2011–12 season, Duffy's Clyde defeated his ex managing team Brechin City 4–2 away and East Stirlingshire 7–1.
[19][20] Nairn County of the Highland League knocked his Clyde team out of the Scottish Cup after a replay in October 2012.
[21] Duffy was awarded manager of the month in League Two for October 2013 after an unbeaten month with Clyde in the league and Scottish Cup,[22] The team stretched that unbeaten run to ten games between October and December,[23] but a 3–1 home defeat to Peterhead on 7 December ended that run.
[32] He eventually led the Ton to the Scottish League One title which was clinched on the final day in a closely fought contest in the 2014–15 season, his first silverware as a manager.
[38] Duffy was sacked on 29 April 2018 after a run of defeats saw Morton fail to make the Scottish Premiership playoffs, finishing 7th in the Championship.
[41] After a difficult start to his time with the club, the Sons ended the 2018–19 season in sixth place in Scottish League One, losing just twice in their final 15 games.
Duffy left Dumbarton at the end of the 2020–21 season, when they avoided relegation by winning play-off ties with Stranraer and Edinburgh City.