In his first season as an NRL head coach, Henry incurred a fine of $10,000 for Canberra by questioning the impartiality of the referee following a round 19 loss to Melbourne Storm in 2007.

[5] Henry was named Dally M Coach of the Year for 2008, ahead of other nominees Craig Bellamy, Ricky Stuart and Des Hasler.

In 2010, Henry had a lean year as North Queensland won just five out of its 24 games, only avoiding the wooden spoon after Melbourne were stripped of its premiership points for salary cap breaches.

[7] However, on 29 July 2013, Neil Henry was informed by the North Queensland Cowboys chairman, Laurence Lancini, that his services would no longer be needed in 2014 despite the club making the finals three years in a row.

Henry re-joined the Queensland Sate of Origin staff in 2020 as an assistant coach to Wayne Bennett in their series win over NSW.