Hughes was born in Wales, but moved quite young with his parents to Liverpool so he could be termed a local player. Fellow Welshman and Liverpool player Maurice Parry recommended John "Geezer" Hughes for a trial at Liverpool and he must have impressed. Hughes played usually as a half-back, only missing three of the 34 League matches in the 1903/04 season. It was an unsuccessful campaign that ended with relegation, the club finishing in seventeenth place only three years after lifting the league title. 

A report in 1904 commented on the Welshman: "Hughes is about the hardest working player at present figuring in League football. He never tires and is seldom beaten. One thing he lacks, however is judgement and a little more of this and Hughes could be classed among the best 'middies' in the country." Hughes only made one appearance for Plymouth on 10 October 1906 still carrying an injury from his Liverpool days. He retired in January 1907. 

Hughes was a lightweight-boxing champion. He was a brave man and boasted a certificate from Royal Humane's Society for life-saving. Hughes saved no less than four people from drowning! Two of these were rescued from the River Mersey and he rescued a child who had fallen into a clay pit.