MCOMS was conceived after an agreement between Government of Nepal and Manipal Education and Medical Group MEMG in 1992.

The MBBS program began in December 1994 with temporary recognition by Nepal Medical Council and Affiliation to Kathmandu University.

The 700-bed Manipal Teaching Hospital (MTH), Pokhara was inaugurated in 1998 by Shree 108 Jagat Guru Shankaracharya.

MCOMS also trains students from United States, Canada, South Africa, Australia, New Zealand, Oman, Kuwait, Saudi Arabia, UAE, Tanzania, Kenya, and the Maldives.

On completion of three academic years and on fulfillment of all university requirements including thesis and exam, the candidate is awarded MD/MS degree.

[1] MTH is the largest hospital in Western Nepal and serves as tertiary care referral center.

Manipal College of Medical Sciences (MCOMS) is also recognized by the British Columbia & Ontario Student Assistance Program (BCSAP & OSAP), Canada.