Cowie came up through Ross County's youth system and went on to captain the club. His father was also a footballer for Ross County. On 30 January 2007, he signed a pre-contract agreement with Highland derby rivals Inverness and officially joined them on 1 July 2007.
Cowie's first season at the club proved fruitful as he abided so quickly to the Scottish Premier League (SPL). He scored his first goal for the club in a 2–1 defeat away to St. Mirren. During Caley Thistle's poor start to the season Cowie proved to be an inspirational figure in the starting eleven. One of his best moments of the season came when he scored the third, and winning goal in Caley Thistle's 3–2 win over Celtic, as well as a stunning 20 yard volley in a win over Kilmarnock. He finished the season as Inverness' top scorer with nine goals and was voted Player of the Year in Caley Thistle's match program.