Mooney's first job in RTÉ was during the 1984 Summer Olympics in Los Angeles when he acted as a Runner, working through the night.

Mooney has saved at least two men from certain death during his lifetime. In the early 1990s, he rescued a man who was drowning in Clontarf, Dublin. In 2012, he scaled up a bridge and bounded across a County Meath motorway “like Superman” to save the life of a 57-year-old man whose collapse had left him “lying flat on his back with blood coming out of his nose and his mouth”. Mooney began pumping the man's chest and eventually brought him back to life. Mooney and this man appeared together on Liveline with Joe Duffy the following day.

Mooney was one of the presenters of RTÉ children's television shows Echo Island from its inception in 1994 up until he left the programme in February 1996. He presented Gridlock later in the 1990s.

First broadcast in 1995, Mooney is a radio programme on RTÉ Radio 1. Originally called Mooney Goes Wild On One, it focused on nature and wildlife, aired at weekends on RTÉ Radio 1, but in October 2006 it became simply Mooney, and the format changed to general chat and discussion and was given a regular weekday slot initially for two hours, then reduced to ninety minutes in 2007.

After Mike Murphy retired from Winning Streak in 2001, Mooney became the new presenter of the Saturday night game show, but was temporarily replaced by Laura Woods while he presented You're a Star from December 2005 and March 2006. In 2004, he was nominated for the Television Personality of the Year Award at the Irish Film and Television Awards. In addition to all of this Mooney has also presented and produced RTÉ's Liveline, as well as various religious and daily magazine programmes.

Mooney is an avid nature lover. Originally from Donnybrook, he is unmarried and resides in Kilmacud, a south Dublin suburb. His brother David died aged 44 in January 2007. He has nephews and nieces but would prefer not to have children of his own despite saying he "might marry a woman yet". He came out as openly gay in 2012. In interviews he lists his hobbies as travel, cinema, going to the gym and socialising in The George. He exercises in the gym because of his 6.2 cholesterol level. He is a close friend of Alan Hughes and was best man at his wedding to Karl Broderick. In 2012, he had a guest starring role in the comedy series Mrs. Brown's Boys.

In 2008, Mooney hosted the Lotto's first Millionaire Raffle draw during a break in the Rose of Tralee. There was subsequently a major controversy and a National Lottery spokesperson was attacked over the manner in which the draw was conducted, i.e. not live, plus the coincidence that one of the new millionaires was from Tralee.

Mooney announced the points given by Ireland to other nations in the Eurovision Song Contest in 2009, 2010 and 2011, just as he had previously done in 2000. He has become directly associated with this role in Irish life. He has expressed regret at not having had an opportunity to present The Late Late Show.

In 2010 he presented Fame: The Musical, an RTÉ reality talent competition, and in 2011 he presented The Genealogy Roadshow. He dressed up as a leprechaun to beat a world record set by American talk show host Jay Leno. People came from Italy, Poland and Romania to participate. He hosted Mooney Tunes for RTÉ over Christmas 2011, an obvious pun on the similarity between the presenter's name and the word "Looney" as used in Looney Tunes, the Warner Bros. animated cartoon series.

In 2012 he presented RTÉ's quiz show Who Knows Ireland Best?.

Mooney has constant incurable tinnitus in his left ear, stemming from when he had a wet shave where "some kind of electronic device for massaging your face afterwards" was used on him. He felt a vibration jolt through his jawbone. Then there was "the 'zzzz' sound and it never leaving me". Because of this he leaves a television or radio switched on at night. He sleeps for four hours. In 2013, he spoke of his intentions to "end his life" if he were ever to be diagnosed with a terminal illness, stating he made the decision after seeing his mother and brother suffering agonizing deaths.

In February 2015, he took up the post of executive Producer of RTÉ Radio 1's nature and wildlife programming.