Nõo was first mentioned in 1319 as Nughen and as a separate church parish in 1483, during the times when it belonged to the Bishopric of Dorpat. Nõo St. Laurence Lutheran Church is believed to have been built around 1250s to 1260s.
According to Bengt Gottfried Forselius schooling took place in Nõo already in 1686. Since 1688 a local parish school has been working in Nõo. In 1953 the primary school was reorganized as a secondary school. In 1965 a computing centre was established, the school was given the first school computer in the USSR – the Ural-1. In 1994 Nõo school was separated into Nõo Secondary Science Gymnasium and Nõo Primary School.