Namuna Machhindra Secondary School was founded on Mangsir 21, 2008 BS. It started as Machhindra Middle School and later became Machhindra Institute after gaining high school status. In 2033 BS, the school merged with Namuna Model Primary School, adopting the name Namuna Machhindra Secondary School. Namuna Machhindra Campus was established in 2037 BS to offer higher education opportunities within the school premises.