Muruaki secondary opened in 1986 as a day mixed secondary school. The first Head teacher was Mr. J. Gitero . Its establishment was an initiative of the local leaders led by the Area chief Mr. Machua . They mobilized the parents in the neighboring primary schools i.e Rugongo, Muruaki and Faru in buying a 15 acre piece of land on which the school is situated. Its 1st structure which included 2 classrooms were constructed through harambee.
Since it inception,the school has seen remarkable growth from a student enrollment of 12 to the current 455.It has been managed by five principals and Mr. Khisa Francis is the current one since year 2016.The school transisted from a mixed school to a Boys’ school in the year 2014 and is three streamed. Muruaki boy secondary school is a public boys school.