Kedah is the oldest state in Malaysia and was the earliest state to practice the Islamic system of government. This system of government was introduced by the first Sultan of Kedah who embraced Islam and started implementing Islamic law in governing the state, namely Sultan Al Muzaffar Shah I (1136-1179). Under this system of government, the Sultan became the head of the government and the head of the religion of Islam. At that time, religious scholars were appointed as advisers on Islamic religious affairs and they were called Guru Sultan.

The role of Guru Sultan was enhanced during the reign of His Royal Highness the 24th Sultan of Kedah, namely Sultan Ahmad Tajuddin Mukarram Shah ibni Almarhum Sultan Zainal Rashid Al-Mu'adzam Shah I (1854-1879) by dividing the role of Guru Sultan into three main divisions, namely Mufti, Kadi and Imam. Later, during the reign of His Royal Highness Paduka Sri Sultan Abdul Hamid Halim Shah Ibni Al-Marhum Sultan Ahmad Tajuddin Mukarram Shah (1881-1943), the 26th Sultan of Kedah, the roles of these three divisions were merged under a special religious institution placed under the administration of the state government and named as the Pejabat Agama Negeri Kedah. Pejabat Agama Negeri Kedah deals with the Islamic affairs in the state of Kedah generally and specifically with matters regarding marriage and divorce. It is led by a Syeikhul Islam appointed by the Sultan.

The structure and function of Pejabat Agama Negeri Kedah was further streamlined under the reign of His Royal Higness the 27th Sultan of Kedah, Sultan Sir Badlishah ibni Almarhum Sultan Abdul Hamid Halim Shah (1943-1958) in 1952. Pejabat Agama Negeri Kedah was renamed as Majlis Agama Islam dan Adat Istiadat Melayu. Majlis Agama Islam dan Adat Istiadat Melayu consists of a chairman called Yang Dipertua, a Secretary and 22 members consisting of 11 State scholars and 11 Malay customs officials.

During the reign of Al-Sultan Al Mu'tassimu Billahi Muhibbuddin Tuanku Al-Haj Abdul Halim Mu'adzam Shah ibni Almarhum Sultan Badlishah (1958-2017), the 28th Sultan of Kedah, Majlis Agama Islam Negeri Kedah was established to replace the role of Majlis Agama Islam Negeri dan Adat Istiadat Melayu.

The establishment of the Majlis Agama Islam Negeri Kedah was effected on 4 April 1963, corresponding to 11 Zulkaedah 1382 through the enforcement of the Administration of Islamic Law - Kedah State Law No. 9 of 1962. Then, the Majlis Agama Islam Negeri Kedah was declared as an official institution which takes care of Islamic religious affairs in the state of Kedah in 2008 under the Administration of Islamic Law Enactment (Kedah Darul Aman) 2008.

The reform that was made in 2008 relates to the appointment of the President of the Council being no longer the Director of the Jabatan Hal Ehwal Agama Islam Negeri Kedah (JHEAIK), but instead was appointed directly by the reigning Sultan of Kedah. Since then, the name of the Majlis Agama Islam Negeri Kedah or its abbreviation MAIK has been used until now.