Mutonguni Secondary School started way back in 1936 as the first Primary School in Mutonguni Location under African Inland Mission (AIM). It is Located in Mutonguni Location approximately 25 kilometers from Kitui Town along Kitui –Kabati- Mwingi Road in Kitui West District. The school attracted pupils from all over the corners of the location and even beyond including Migwani and Matinyani.In 1952 the School was elevated to the intermediate School status. In 1966 the School admitted the first form one class as a mixed school under the Harambee stream admitting both boys and girls. In 1970 the school was upgraded and became a Government aided day Secondary School however authorized to admit boys class.
Students rented rooms in the neighboring Tulia Market while others commuted from their homes while a few stayed in private hostels. In 1979 the school got the second boys stream and in 1980 an official form one girl’s stream was established being fully boarding making the school a triple stream. The school became a full boarding school in the year 1985 and it admitted the first ‘A’ level class in 1986 which went on until 1989 when they were phased out.