 Due to the different time-frame of the League of Ireland season, the end of the 2008–09 campaign brought Mooney his first break from playing and training since March 2008.On 16 October 2009 it was announced that Mooney would be joining League One side Charlton Athletic on an emergency loan until 1 December.He made his first team debut the next day, coming on as a late substitute in Charlton's 2–1 victory against Huddersfield Town at The Valley.