Having represented Ireland at the Under-19 World Cup in 2000, John Mooney made his debut in the 2004 ICC Intercontinental Cup against the Dutch. He played his second game after a gap of nearly two years and was also part of the EurAsia cricket series and the CAG Trophy in the same year.

Mooney played in Ireland's first-ever ODI in 2006 against England where he put in an impressive show picking 3 crucial wickets and also scoring 30 off 26 deliveries. He was part of the Irish squad in the 2007 ICC Cricket World Cup after which he took a break from international cricket in order to complete his electrical apprenticeship. In 2009 Mooney was named captain of the victorious Ireland A squad for the European Cricket Championships where he was named player of the tournament. He was singled out by the national team coach as the stand out performer at the 2009 ICC World Twenty20. For the 2009/10 season Mooney moved to Australia to play club cricket in a bid to play the longer format of the game. In Jan 2011 he was named Ireland's Player of the Year for 2010. He was part of the Irish squad at the 2011 ICC Cricket World Cup.