Dumbarton born outside left John Cowan began his football career with Vale of Leven and joined the stream of Scottish footballers playing in the English League in the summer of 1892, when he joined First Division Preston North End, making his Football League debut at Derby County that September. He missed only four matches as Preston finished runners up in the League Championship and played for Preston in the 1893 FA Cup semi final, its replay, Cowan scoring in a 2-2 draw, and its second replay, in which they were ultimately defeated 2-1 by Everton at Ewood Park. He was a near ever present in 1893-94, missing only one match and scoring 4 goals in Preston’s 18-0 FA Cup first round rout of Southern League Reading in January 1894.
After 16 goals in 64 appearances for The Lilywhites he joined Glasgow Rangers in the 1894 close season, making his Rangers debut against Dumbarton that August, and scoring 4 goals in 17 appearances before a return to England to join his younger brother Jimmy Cowan at Aston Villa the following August.
Aston Villa won the League Championship in 1895-96. Cowan scored 9 goals in 22 games that season, and was part of a foward line that included Johnny Campbell, John Devey, Charlie Athersmith and Dennis Hodgetts. As Philip Gibbons pointed out in Association Football in Victorian England: “Aston Villa had twice won the League Championship, as well as the FA Cup, during the three previous seasons, with a team generally acknowledged as the finest in the land.”
The following season proved the most glorious for Aston Villa. On 30th January, 1897, Aston Villa beat Newcastle United 5-0 in the third round of the FA Cup. They went onto beat Notts County (2-0), Preston North End (3-2) and Liverpool (3-0) to reach the Cup Final against Everton. A crowd of 60,000 arrived at The Crystal Palace to watch the Final. Charlie Athersmith scored the opening goal but Everton hit back with goals from Jack Bell and Richard Boyle. Aston Villa continued to dominate the game and added two more goals from George Wheldon and Jimmy Crabtree. That finished the scoring and therefore Aston Villa had emulated the great “Invincibles” Preston North End side that had achieved the FA Cup and Football League double in 1888-89 season. Aston Villa retained the League title by beating the runners up, Sheffield United, by an amazing 11 points. Aston Villa scored 73 goals that season with Cowan scoring 7 in 15 games.
However 1897-98 proved a disappointment, and Villa finished only sixth in the League, crashing out of the FA Cup in the first round, although Cowan still featured regularly. The following season however, as a result of the form of Stephen Smith, Cowan was unable to obtain a regular place in the 1898-99 League Championship winning team. only playing 7 games that season. After 27 goals in 71 appearances for Villa, Cowan moved to Dundee Hibernian in June 1899 before his eventual retirement in May 1901.
He was the older brother of Aston Villa stalwart and Scottish international James Cowan.