After he left school a strong season for the Mataura Rugby Club saw him selected to play provincially for the Southland Stags in 2000.
He was quickly recognised as a standout in a weak Stags side and after a good season in 2002, he received a call-up to the Highlanders super rugby franchise.
His form with the Southland side benefited from his experience at a higher level of rugby and the Stags back line continued to improve.
In 2004, after a great National Provincial Championship competition, Cowan received an All Black call-up for the 2004 end of year tour after becoming the youngest Southlander to bring up 50 games for the province at the age of 22.
In 2007 after missing out once again on the All Blacks Cowan made a strong impression for the Stags helping them to reach the quarter final stages.
He missed out on the Stags first successful Ranfurly Shield challenge in 51 years against Canterbury where his brother Scott took his place as halfback.
He was mentored by All Blacks Halfbacks Danny Lee and Byron Kelleher, who at the end of the season departed Otago and the Highlanders to play for Waikato and the Chiefs, leaving Cowan and Ben Hurst to battle for the starting role.
[5] Following the 2012 season and after 108 games for the Highlanders, with 26 as captain [citation needed] Cowan made his All Black debut age 22, versus Italy, coming on as a substitute.
[1] On 17 April 2012, Jimmy Cowan would leave the Highlanders to join English side Gloucester Rugby in the Aviva Premiership for the 2012/13 season.
[12] On 14 July 2014, Cowan returned home to New Zealand as he joins Tasman Makos on a one-year contract in their next ITM Cup campaign.
In the 1990s and early 2000s, Southlanders Jeff Wilson, Justin Marshall, Mils Muliaina and Corey Flynn all shifted north to play for larger unions, as they looked to advance their prospects.
At the beginning of his career, Cowan received several enticing offers from Super Rugby host provinces, but knocked them back to remain with the Stags and Highlanders.
[15] Former All Blacks coach Sir Graham Henry said Cowan was one of the most well-respected players in the national squad and that he had the rare ability to relate with everyone in the team.