Santos started as a local 6-aside team based in Oldham in the late 1990s. In 2006, after years of dominating the various competitions, several of the players decided to form an 11-aside team and Santos AFC was born.

In their first ever season Santos entered the Rochdale Online Alliance League Division 2 and were duly promoted and reached the League Cup semi-final. They also won the Rochdale Observer Sportsmanship Trophy for fair play.

In their second season the Club expanded and added a reserve team and under 14s youth team. The first team went one better that season and reached the League Cup Final but competitive silverware still eluded them as they lost an exciting final 4-3.

At the start of the 2008/09 season Santos joined the Lancashire & Cheshire League as they continued to develop and progress the Club.