From 2004-2005, Lenihan was the assistant coach of the Burleigh Bears' FOGS Colts side.[5]
In 2006, Lenihan was appointed as head coach of the Bears' Queensland Cup side, replacing Rick Stone, who eventually joined the Newcastle Knights as an assistant coach.[6][7] After making three straight Grand Finals under Stone, the Bears missed the finals for four straight seasons under Lenihan, with sixth being their highest finish. He resigned from the club at end of the 2009 season.[8]
In 2011, after a year away from coaching, Lenihan joined the Bilambil Jets, winning the Bycroft Cup in his first season at the club.[7] In December 2013, he rejoined Burleigh as an assistant coach after three seasons with Bilambil.[9]
In May 2014, Lenihan became head coach of the Bears for the second time, replacing Carl Briggs.[10] In 2016, the Bears won the Queensland Cup Grand Final, defeating the Redcliffe Dolphins 26–16 at Suncorp Stadium.[11] In 2019, Lenihan won his second Queensland Cup Grand Final with the Bears, defeating the Wynnum Manly Seagulls 28–10 at Dolphin Stadium.[12]
On 8 October 2019, he joined the Gold Coast Titans as an assistant coach on a three-year deal.[13]
On 22 June 2023, Jim Lenihan was appointed interim head coach of the Gold Coast for the remainder of the 2023 season after previous Head coach Justin Holbrook departed with the club.[14]
In September 2025, due to the sacking of coach Des Hasler, and the introduction of new coach Josh Hannay, Lenihan left the club, 1 month shy of 6 years at the club. This was because Hannay confirmed that he will field a fresh coaching staff. [15]
On September 24th 2025, following his departure from the Titans, Lenihan became head coach of the Brisbane Tigers, who plays in the Queensland Cup, for 2026 and potentially further. [16]