The 5'10" tall player first began playing for the Home Farm Club in Dublin before signing for Wolverhampton Wanderers in 1998. In 2001-2002 Melligan went on loan to Bournemouth and again at Kidderminster Harriers in 2002-2003. After scoring 12 goals in 31 appearances he returned to Wolves and made two substitute appearances in (the then) Division 1.
In 2003 he made a substitute appearance for the Republic of Ireland Under-21 team and went on to make 21 appearances on-loan at Doncaster Rovers in the 2003-2004 season.
At the end of that season Melligan signed for Cheltenham Town from Wolves for £25,000. He went on to miss just three league games for Cheltenham over the next three years as he became an important part of their side.
On 6 June 2007 Melligan signed for Leyton Orient on a free transfer, and scored in only his second appearance for them. He left Leyton Orient in February 2010 after falling out with manager Geraint Williams following the 5-0 victory over Bristol Rovers. He signed a full time contract for League of Ireland Premier side Dundalk in February 2010. Melligan left Dundalk just before they set off to play Grevenmacher, from Luxembourg, in the Europa League. In his short stint with Dundalk he scored three goals in fifteen appearances.
On 2 July 2010, Melligan re signed for his former club, Cheltenham Town. 'JJ' had a clause in his contract allowing him to leave Dundalk if a Football League club came in for him so he was allowed to leave Dundalk FC for free.
On 9 May 2011, Melligan was released from Cheltenham after his contract expired.