The club was founded as Bunamwaya FC in 1969. Vipers SC have played in the Uganda Premier League since 2006 after winning the Wakiso District and Super Mini League promotion league in 2005. They have finished in the top half of the table every year since the 2006–07 season. With the backing of president Lawrence Mulindwa, the club signed several important players for the 2010 season, including seven members of the Ugandan National Team at the time. Bunamwaya won their first ever Uganda Premier League title with two rounds to spare. They did not participate in the 2011 CAF Champions League for financial reasons. Bunamwaya were unable to replicate their success, finishing 3rd in 2011 and finishing runners up in both the cup and the league in 2012. On 21 August 2012, Bunamwaya was renamed to Vipers SC in order to "elevate the status of the club" and make them more nationally relevant. Vipers lost the 2013 Uganda Cup final in heartbreaking fashion. After taking the lead in the 78th minute on a Joseph Mprade penalty, Victoria University scored a goal in the final seconds of the match and then went on to win the penalty kick shootout 5–3. League success finally came again in the 2014–15 season after a league campaign which saw Vipers lose only once. They were led by Edward Golola. The club has close ties with St. Mary's School in Kitende, with 17 players on the 2015 championship-winning squad from that school. The championship found Vipers in continental competition for the first time. In the 2016 CAF Champions League, they lost their first ever continental tie 2–1 on aggregate to Enyimba FC of Nigeria in the preliminary round. Vipers finished runners up in the 2015–16 season but saw their first ever success in the Uganda Cup, beating Onduparaka FC 3–1. The win qualified them for the 2017 CAF Confederation Cup where they beat Volcan Club from Comoros 1–1 on away goals in the preliminary round but fell to South AfricanPlatinum Stars in the first round 3–2 on aggregate after conceding a 90th minute penalty. The Vipers participated in the 2018-19 CAF Champions League where they fell to CS Constantine of Algeria 3–0 on aggregate, one round shy of the group stage.
In may 2020, Vipers sc was declared champions of the Uganda Premier League 2019/2020 while leading with 54points from 25 matches for the fourth time in their history after the league was cancelled by FUFA due to the out break of COVID19 disease.
Stadium
They play at St Mary's Stadium Kitende, which has a capacity of 20,000. The stadium was completely refurbished in 2018 and includes artificial turf.
