MSS was inaugurated as a result of a shortage of secondary schools, especially in anticipation of the record number of primary-school leavers in January 2000.

Choy Chee Meh was appointed the first principal of MSS,[1] and acquisition of land at the current site began shortly after the decision to establish the school.

Primary-school leavers had little interest in choosing MSS at first, compared to the other long-established secondary schools in the Woodlands area.

During this period, MSS hosted three Edu-Pi camps, a two-day educational workshop to encourage the use of Apple Inc.'s products such as iMovie and the Mac OS.

[1] MSS merged with Si Ling Secondary School with effect from 1 January 2017 due to its small student population.