The club was established in Heideveld on the Cape Flats in 1982 and was originally known as Lightbodys Santos FC. During apartheid it was renowned for the insistence on non-racial inclusivity – hence the nickname The People's Team.
The NSL became the PSL in 1996, with Santos earning promotion to the new league for the 1997-98 season. Santos tasted their first success in the new format of the league in 2001–02 when they surprisingly won the title under the mentorship of Gordon Igesund. This side featured players like Edries Burton, Andre Arendse, Musa Otieno and the club's all-time top goalscorer Jean-Marc Ithier. With the title win Santos became the first - and to date the only - team that was not a founder-member of the PSL to win the league.
Santos were relegated from the PSL at the end of the 2011-12 season for the first time in the club's history. After finishing 15th in the league they entered the 2011-12 PSL Playoff Tournament where they were pitted against Chippa United and Thanda Royal Zulu. Heading into their final playoff game Santos needed a win over Chippa United to maintain their PSL status but they were defeated 4-3 and subsequently relegated, with Chippa United taking their place in the PSL.