The club was founded in 1891, and they become known as the Aberavon Excel, playing in an all-white strip. After the First World War in 1918, the Excels formed the Aberavon Harlequins R.F.C. which it has been known as ever since. They played on a waste site at what is now the Sandfields Estate, later renamed the Harlequins Field. In 1932-33, the club was reformed by Dick Lody, Dill Stanford, Don Mainwaring and H.Williams, and the club grew until the start of Second World War.
In 1951, the club received a boost when the former Maesteg RFC, Wales and British Lions scrum half Trevor Lloyd returned to Aberavon Harlequins, his original club. The 1955/56 season was the best ever playing record in the Quins' history, playing over thirty matches and losing only once.
At the start of the 21st century, in an attempt to modernise the governing body of Welsh rugby union and to bring Wales fully into the professional era, it was decided to restructure the Welsh leagues and to source new sponsorship revenue for them. Teams would be allocated a division depending on their recent season’s order of merit and their geographical location. In the 2001/02 season, the Quins were placed in Lloyds TSB Division Two West, along with their local rivals Corus (Port Talbot) RFC.