In 1980, Lowney released Wavelength, a 17-minute short subject about pirate radio in Dublin that he directed and produced. It won the Critics Choice for Outstanding Irish Film at the 1980 Cork Film Festival. Throughout the 1980s, he worked for Irish national broadcaster RTÉ including as a producer on the show TV Ga Ga (1985). He became known for directing musical events, including the 1988 Eurovision Song Contest, for which he won a Jacob's Award. Lowney courted controversy shortly before the contest, when he stated in an interview that Eurovision was "just an excuse for a load of TV executives to go on the piss on expenses". Into the 1990s, he directed the Bob Marley biopic Time Will Tell (1991) and The Velvet Underground's 1993 tour Live MCMXCIII.
After directing some Penn and Teller shows and the Jo Brand series Through the Cake Hole, Lowney met with writers Arthur Mathews and Graham Linehan about directing a new sitcom they had written called Paris. He did not get the job, but Matthews and Linehan remembered him when they were putting together a production team for their next sitcom, Father Ted. Lowney took input from Linehan and Matthews on set, and the three often refined the scripts during filming. One of Lowney's favourite episodes is "Song for Europe", which mocks the frequency Ireland wins the Eurovision Song Contest, and features a music video scene. For his work on two series and the Christmas special, Lowney was the co-recipient of the 1995 BAFTA Television Award for Best Comedy (Programme or Series). Lowney was met by Christine Langan, a Granada Television producer who wanted him to direct Cold Feet, an ITV Comedy Premiere. Lowney agreed and Cold Feet was filmed in 1996, though not broadcast until 1997. It was a success, winning the Golden Rose of Montreux and a British Comedy Award. Langan asked Lowney if he would like to return to direct the first two episodes of the recently commissioned series of Cold Feet. He declined the invitation because the production schedules clashed with his first feature film, Mattie. Written by Hugh Leonard, Mattie was to star Terence Stamp and Mia Farrow. Funding for the film fell through the week before principal photography was due to begin. Lowney was offered the first episodes of Cold Feet again and this time accepted. The episodes were broadcast in 1998.
After the failure of Mattie, Lowney finally got the chance to direct a debut feature with Wild About Harry (2000). The following year, he directed the first series of Paul Whitehouse's Happiness, which was nominated for a BAFTA. He returned for the second series in 2003. In 2005, he directed Whitehouse's Help, and the third series of Little Britain. Help won Lowney his second BAFTA and Little Britain secured him another nomination. In 2008, he directed a major television advertising campaign for Reveal magazine. In 2009, he directed the RTÉ sitcom Never Mind the Nursing Home and three episodes of the ITV romantic comedy Married Single Other, which were broadcast in early 2010. In 2010, Lowney directed a performance of Riverdance in Beijing in high-definition. The performance was scheduled for release on Blu-ray to mark 15 years of the troupe.
Lowney played a role developing Eddie the Eagle, a biographical film about Eddie 'the Eagle' Edwards, and was reportedly set to direct. However the film was eventually directed by Dexter Fletcher.
In 2013 Lowney directed Steve Coogan in the Alan Partridge feature film, Alan Partridge: Alpha Papa.
