Maktab Sains Paduka Seri Begawan Sultan began as Sekolah Menengah Melayu Pertama (SMMP) in Brunei Town in 1966. In 1967, the Upper Secondary Level was introduced. Before this, there was only Lower Secondary Level in Maktab Sains.
Two years later, the school was moved to Jalan Muara and Sixth Form classes started. On 23rd September 1971, Maktab Sains Paduka Seri Begawan Sultan was officially named Maktab Melayu Paduka Seri Begawan Sultan and was inaugurated by Al-Marhum Sultan Haji Omar Ali Saifuddien, the 28th Sultan of Brunei. In 1974, the bilingual education policy was implemented and English Medium Classes was introduced.
However, starting 1976, there were both English and Malay medium classes right up to form 5. In 1978, Maktab Sains Paduka Seri Begawan Sultan provided Science education as the concept of institution. Since then the school's name was changed to Sekolah Sains. Hostel facilities for both boys and girls were also provided.
In 1985, the reputation of the school was developed to that of a college to acknowledge the inclusion of the Sixth Form. With this, the school was officially renamed MAKTAB SAINS PADUKA SERI BEGAWAN SULTAN
Maktab Sains Paduka Seri Begawan Sultan was one of the two colleges in Brunei chosen to launch the full day schooling scheme.
In 1994, MSPSBS was moved to a new campus site in Kampong Rimba Gadong as the premise ind Jalan Muara were under construction.
On 2nd April 2005, MSPSBS site was moved back to Jalan Muara after 11 years sited at Rimba. The college for the first time scheduled Menengah 1 in the afternoon session in 2007.
In 2008, both Form 2 and Year 7 were scheduled in the afternoon due to the insufficient classrooms. Year 7 of 2008 was the first batch to try out the scheme of work for SPN 21.
