Muhyiddin School is named after the king, Al Sultan Mohamed Muhyiddeenul A’dil Siri Naakiree Sundhara Mahaaradhun, who ruled the country from 1691 to 1692. He was an eminent scholar and a prominent intellectual who contributed a great deal to improve the education and religious awareness in the country. Scholars were exceedingly respected and recognized by His Majesty as a high concern.

The school was initially opened on 8^th March 1994 with two teachers and fifteen students. At the outset, two bungalows, which were built for the purpose of tourism, were used as school premises. Multi grade teaching was carried out in these classes.

As the school enrolment increased rapidly, government decides to construct new buildings and upgrade the school. The former Minister of education Doctor Mohamed Latheef laid the foundation of the first phase of the school on 16 June 1996.Under the project, five temporary classrooms were built in 1998 and another four-story building was constructed in 2000 to meet the inadequacy of classroom and other facilities. The former President of Maldives His Excellency Maumoonu Abdul Qayyoom, officially inaugurated Muhyiddin School on 7^th June 1999.