This article attempts to explore the relationship between Qur’an schools or classes and vernacular Malay schools, as also the metamorphosis of the native educational system into a modern rational institution. This transformation process initially commenced as a personal initiative of some British administrators such as Thomas Stamford Raffles and R. J. Wilkinson, and eventually led to an overhaul of the existing educational system into an organized secular format by the authorities of the British colonial administration around the second part of the 19th century. The rational basis of the establishment of Qur’an schools or classes was a direct impact of being a Muslim community. After accepting Islam as the ‘national religion’, Malays initially adopted the Arabic alphabet as their writing script in a common cultural and religious process experienced in almost all Islamic communities around the world. Since Islam is regarded as the source for acquiring practical knowledge in daily community life, Malays established Qur’an schools in order to educate their future generations. In the process, the implementation of this system of education created its own tradition and was internalised within the community. However, the arrival of the British as colonialists altered the scenario somewhat. They were regarded as catalysts in the transformation of Malay society, spearheading their thrust first by making inroads into the existing system of education. Planned as a short view on the issue, this treatise has a limited focus on general policies, and on some distinguished figures such as Thomas Stamford Raffles, Frank Swettenham and especially Richard J. Wilkinson who are perceived as having taken the initial initiatives on the setting up of Malay vernacular schools. The research is based on the period starting from approximately the beginning of the 19th century, and its direct results on the developments concerning educational transformation until the first decades of the 20th century. The attempts of the aforementionedBritish officials at social engineering in Malaya, through the establishment of vernacular schools,contributed to the transformation of the traditional Qur’an schools.