Following the departure of John McCormack to Morton in November 2002, former player Kenny Brannigan was appointed as head coach in January 2003.
Since leaving Queen's Park in 1986 Brannigan had seen service at 13 other clubs, including Sheffield Wednesday, Stockport County, Stranraer, Clydebank, Falkirk, Kilmarnock, Partick Thistle, Berwick Rangers and Stirling Albion.
His first game in charge at Hampden saw Queen's throw away a two goal lead against East Stirling at Hampden, and Queen's won just two games in the remainder of the season.
Season 2003/04 started off well, and after being denied victory over first division St Mirren by a penalty two minutes from time, Queen's took on eventual First Division winners, Scottish Cup semi-finalists and Challenge Cup winners Inverness CT in Inverness.
Against the odds Queen's came from a goal behind to record a famous 2-1 victory with a Stevie Reilly penalty and an Ally Graham strike, undoubtedly the club's best cup result since putting Premier Division Ayr United out of the Scottish Cup in the mid seventies.
However, Queen's finished the season with ten league victories in seventh place.
Season 2004/05 started off well following a week's training camp in Cattollica, Italy, and a penalty shoot out win over Stenhousemuir in the Challenge Cup was followed by two goals in the last three minutes to record a 3-2 win over Cowdenbeath.
However, in the following league game at Elgin City, an incident involving David Clarke after his substitution was followed by an altercation with a supporter, and his contract was terminated the following week.
Following spells as assistant to Sandy Stewart at Airdrie United and Gordon Chisholm at Queen of the South, he took over the Dumfries side in 2010. However, the Dumfries side declined to extend his contract once the 2010/11 season finished.
In March 2012 Brannigan went overseas, and took over as Manager of Pheonix SC in Winnipeg, Canada.