Perlis was originally part of Kedah, although it occasionally came under rule by Siam or Aceh. After the Siamese conquered Kedah in 1821, the British felt their interests in Perak to be threatened. This resulted in the 1826 Burney and Low Treaties formalising relations between the two Malay states and Siam, their nominal overlord. In the Burney Treaty, the exiled Kedah sultan Ahmad Tajuddin was not restored to his throne. Sultan Ahmad and his armed supporters then fought unsuccessfully for his restoration over twelve years (1830-1842).
In 1842, the Sultan finally agreed to accept Siamese terms, and was restored to his throne of Kedah. However, Siam separated Perlis into a separate principality directly vassal to Bangkok. Syed Hussain Jamalulail, the paternal grandson of a Hadhrami Arab immigrant and maternal grandson of the Sultan of Kedah, became the first Raja of Perlis. His descendants still rule Perlis, but as rajas, instead of as sultans.
As with Kedah, the Anglo-Siamese Treaty of 1909 forced Siam to relinquish its southern Malay vassal states to Great Britain. The British installed a Resident in the Perlis royal capital of Arau. Perlis was returned to Siam by the Japanese in World War II as a reward for Siam's alliance with Japan, but this brief annexation ended with the Japanese surrender. After World War II, Perlis returned to British rule until it became part of the Malayan Union, then Federation of Malaya in 1957 and lastly Federation of Malaysia in 1963.
Since 2000, the Raja or hereditary monarch has been Tuanku Syed Sirajuddin. He was the Yang di-Pertuan Agong of Malaysia from 2001 to 2006. Tuanku Syed Faizuddin Putra was the Regent of Perlis during the five-year period when Tuanku Syed Sirajuddin was Yang di-Pertuan Agong. The Chief Executive or Menteri Besar is Datuk Seri Dr Md Isa Sabu of Barisan Nasional.