It was established in 1973 under the Second Malaysia Plan as the first boarding school (Sekolah Berasrama Penuh) in the state.

[12][13] This school, formerly known as Sekolah Menengah Sains Melaka,[14][15][16] was established in a hilly area with a height of 121.9 meters above sea level.

[18] Due to the slow completion of the Muzaffar Syah Science Secondary School building, the students were transferred to Sekolah Menengah Sains Johor in Kluang the following year.

[24][25] In 2001, the Al-Abrar surau was built and inaugurated by the Yang di-Pertua Negeri Melaka as well as the construction of spotlights in schools, hostels and fields.

In 2007, the MOZAC field became the training ground for Manchester United for the 2007 Youth Champions Cup and was also upgraded to a 5 Star Sekolah Bestari.

Since then, MOZAC have 2 classes of Dual-Language Programme (DLP) in each grade which used Malay and English as communication language.

They are responsible for managing cleanliness and supervising programs such as the recitation of Surah Al-Kahfi on Fridays.

Earlier, when it was awarded the Cluster School status, there were three niche areas: k-teroka (R & D), e-MOZAC (ICT) and e-Tinta (Writing).

In 2009, the school produced its own thumb drive known as i-MOZAC (not to be confused with Apple's products).

Recently, the school started to do research involving the potential of green technology.