Cowan made his Test debut for the All Blacks against Italy in 2004 at age 22, having made his Super Rugby bow for the Highlanders the previous year.

The Southland No.9 was not capped again until a year later but was part of the All Blacks' 2006 Tri-Nations-winning squad in 2006. The following year, Cowan found himself demoted to the Junior All Blacks and therefore missed out on selection for the Rugby World Cup.

However, his strong Super Rugby form for the Highlanders saw him named as New Zealand's Super 14 Player of the Year in 2007 and he soon found himself back in All Blacks contention. Cowan's resurgent form on-field was tempered by disciplinary worries off it, as he was fined by the New Zealand Rugby Union and banned from drinking alcohol after three drink-related disorderly behaviour charges were brought against him in the space of three months.

Cowan turned his personal life around during 2008, nailing down the starting No.9 berth as the All Blacks wrapped up another Tri-Nations title before completing a Grand Slam tour of the UK. In January 2009, his rehabilitation was given a further boost when he was named as the Highlanders captain for that year's Super 14 campaign.

He was a key figure for the All Blacks that year and the next and his strong run of form led to a new two-year deal with the NZRU and the Highlanders. In 2011 the Highlanders captaincy was passed to Jamie Mackintosh and Cowan responded by playing arguably his best Super Rugby season that was rewarded with a place in the All Blacks' World Cup squad.

He made his 50th Test match outing against Canada in the pool stages of the competition but had slipped down the pecking order behind Piri Weepu and Andy Ellis by the time the All Blacks lifted the Webb Ellis Cup.

His stock also fell on his return to domestic matters with the Highlanders and as his contract came to an end he was heavily linked with a move to English Premiership side Gloucester.