The school was formerly known as the Singapore High School of Science was founded in the hills with a height of 121.9 meters above sea level. Originally Area is 12.9 hectares. The history of this school was started on January 5, 1973. On this date, a total of 120 students from Form 1 consisted of 80 male and 40 female students as a pilot was placed in the Secondary School Munshi Abdullah , Batu Berendam, Malacca , while waiting for the school building was completed.
On January 3, 1976, a total of 120 students from Form 1 has been superimposed on one another in High School Munshi Abdullah .They were placed in the Secondary School Science Muzaffar Syah, Melaka on May 10, 1976. In 1978, with collaboration from the Matriculation of the University Kebangsaan Malaysia (UKM) this school has been entrusted to conduct the Matriculation course, one year intensive course for students of Universiti Kebangsaan Malaysia.The first group of students matriculation course consists of 102 students who come from all over the country. Form 6 UKM Matriculation classes were discontinued and re-connected with the launch of Engineering Science matriculation classes.
October 1983, the school was originally the name of Singapore High School of Science was officially changed to the Muzaffar Syah Science Secondary School, named after the Sultan of Malacca Sultan Muzaffar Shah of the fourth. Opening the name change was completed by His Excellency the Speaker of the State of Melaka , Tun Syed Zahiruddin
Making the school population is constantly being built and faith centered on science by the year 2020
Providing comprehensive quality education to produce competent young, competent, generous attitude and believe in public service and private sector based on FPN.
Surely these students are capable of high potential for further development towards achieving excellence on the faith and obedience to God. So the opportunity is given to them to promote and develop their talents to become a knowledgeable person, personal moral responsibility, religion, society, nation and state.