Machhindra FC was established in 1973.[5] For sponsorship reasons, it was named Machhindra Bahal Club in 2004,[6] and Machhindra Energizer FC in 2006.[7] The club was promoted to Nepal's top football division in 2004. The team was one of the first teams in Nepal to appoint a foreign coach, Johan Kalin, in 2013, claiming that he was the highest qualified coach in Nepalese football history.[8] He led the team to a second-place finish in the league, and was praised for his tactics.[9]
The beginning of the 2020s started the clubs most successful time with two consecutive league championships.