Molloy started his league career with
Shamrock Rovers at 18 making his
League of Ireland debut at St Mel's Park on 7 January 1996 but after only a handful of appearances he moved to
First Division club
Athlone Town in 1996. He immediately hit his stride and ended up the division's second top scorer in
1996–97 season earning him a move to
St Patrick's Athletic and a shock call up by
Brian Kerr to the
Republic of Ireland national football team for the
1997 FIFA World Youth Championships. Molloy played every game and was Ireland's joint top scorer (2) as they reached the semi-final stage only to lose to eventual winners Argentina. Ireland won
bronze medals after beating
Ghana in the 3rd/4th place play-off game. At St. Pats he linked up with Ireland teammates
Colin Hawkins and
Thomas Morgan, who had been added to the nucleus of the squad that had won the
1995–96 League of Ireland Premier Division, and a lot was expected of the obviously talented squad. All three players made an immediate impact with Molloy enjoying a terrific partnership with
Ian Gilzean as St. Pats won the league with a dramatic last day win in
Kilkenny while arch-rivals
Shelbourne lost to
Dundalk. During this season Molloy won the first of his Under 21 caps. In
1998–99 Molloy finished as the
League of Ireland Premier Division top scorer as St. Pats raced to another league title. After a disappointing 1999–2000 season, Molloy was transferred to
Bohemians for a St. Pats record of IR£40,000. Molloy repaid that fee instantly by scoring the winner as Bohemians knocked out
Aberdeen in the
UEFA Cup. However he then got sent off against
FC Kaiserslautern in the next round. He would go on to play a vital role as Bohs won the League and
FAI Cup double under manager
Roddy Collins. The following year was not as successful for Bohs but they did reach the FAI Cup final only to lose to
Dundalk. In July 2002, Molloy was again signed by Roddy Collins, this time for
Carlisle United of the
English Third Division. After only a handful of appearances yielding a solitary goal against
Lincoln City (a game in which he also got sent off), In January 2007 he joined Motherwell for an undisclosed fee. He left Motherwell by mutual consent in October 2007, having been informed he did not feature in the future plans of manager
Mark McGhee. Molloy signed for Glenavon in December 2007. and was released by the club in June 2011 having not been offered a new contract. ==Honours==