The principal was suspended over poor KCSE results posted in last year’s examinations, following a board resolution on Wednesday.
Mugo was sent home alongside two other senior officials to pave way for an audit of the real cause of the poor performance.
Starehe Boys Centre was ranked 17th nationally, compared to last year when it was ranked fourth, raising serious concerns about the former academic giant in the country.
The school was known to take the top position for several years during the tenure of its founder, the late Geoffrey Griffin.