Born in Jamestown, Dunbartonshire, Cowan was a Scottish international half-back who played with local sides Renton and Vale of Leven before moving to England to pursue a professional career. He joined Aston Villa in 1887 and spent 15 years with the Birmingham side. When Cowan played for the club in the 1890's and early 1900's, they were the giants of the Football League. While at Villa, he won five First Division titles and two FA Cup winners medals. In all he played 354 times for Aston Villa and is considered to be one of the finest players of the Victorian era. He was renowned for his speed. One one occasion he missed a Villa match due to his attending (and winning) the illustrious 100 yard "New Year Sprint" event held at Powderhall. The club fined him but he still made a healthy profit due to the prize money!
After retiring from playing in 1902, he coached the young players at Villa for a few years before deciding to accept the role of manager of Queens Park Rangers in 1907.QPR had just moved to a new ground at Park Royal and Cowan was the club's first official manager. In his initial season he led them to the Southern League title and held Manchester United to a fine 1-1 draw in the Charity Shield.
Four years later he led QPR to another Southern League title. Off-the-field problems however, prevented him from leading the club into the Football League. Prior to the start of the 1913/14 season he offered his resignation on the grounds of ill health which the directors accepted. He returned to Scotland where he died in his sleep in December 1918.