Jigme Namgyel School was established as a Primary School below Changangkha Lhakhang in a private house in 1991. Initially, the Head Teacher (Mr. Tshering Dukpa), along with 17 teachers had managed and led its 400 students. In 1994, the Ministry of Health and Education shifted the school from Changangkha to the place where Motithang School is located now. The name Motithang Primary School was later changed to Jigme Namgyel Primary School. With the construction of a package of buildings under World Bank Project, it was upgraded to a Lower Secondary School on 25th May, 1994.

Ever since the school was established, the following head teachers managed and led the school: Mr. Tshering Dukpa, Ms. Ugyen Lhadon, Mr. Chhimi Weezer (offtg./ Vice Principal) (February-July, 2017), and Mr. Dorji Wangdi (August, 2017- till date) Mr. Dorji came from Kabesa MSS (Punakha ) after being successful from the interview for the post.

Being one of the largest schools with more than a thousand students, the school urged itself to become an Autonomous school for the prompt and qualitative delivery of services. Accordingly, with the government’s policy of decentralization, Jigme Namgyel LSS was offered the Autonomous School status with effect from July, 2015.  Today, its autonomous status better manages and leads the school through the governed principles of transparency, efficiency and accountability.