Men-Tsee-Khang was established in 1916 in Lhasa, Tibet by the Great 13th Dalai Lama and it was re-established on 23 March 1961 by His Holiness the 14th Dalai Lama in Dharamsala, India.

The institute initially started with a doctor and an astrologer with ten students on two separate campuses in Dharamsala called Chopra House and Glenmore Cottage. Dr. Yeshi Dhonden and Ven. Dukhorwa Lodoe Gyatso were the forerunners of Medicine and Astro-Science Schools. In 1967, the two schools were merged together as Men-Tsee-Khang, Tibetan Medical & Astro. Institute in Mcleod Ganj and shifted to the present location in 1982 where the headquarter of the institutes operates.

The 19th batch medical and the 10th batch Astro-science have completed their Kachupa Degrees respectively. Due to the guidance of His Holiness the Dalai Lama to bring out more sowa-rigpa doctors and astro-science practitioners every year led to the expansion of Men-Tsee-Khang (Sowa-Rigpa) College. Thus Men-Tsee-Khang bangalore College has been shifted from Dharamsala to Bengaluru in South India.