AIIMS Jodhpur is one of the SIX NEW AIIMS established by the Ministry of Health & Family Welfare, Government of India under the Pradhan Mantri Swasthya Suraksha Yojna (PMSSY) with the aim of correcting regional imbalances in quality tertiary level healthcare in the country and attaining self sufficiency in graduate and postgraduate medical education. PMSSY planned to set up 6 new AIIMS like institutions in under served areas of the country.

These institutions are being established by an Act of Parliament on the lines of the original All India Institute of Medical Sciences in New Delhi which imparts both undergraduate and postgraduate medical education in all its branches and related fields, along with nursing and paramedical training to bring together in one place educational facilities of the highest order for the training of personnel in all branches of health care activity.

From 2013 onwards AIIMS started admitting 100 MBBS and 60 BSc Nursing(Hons.) students.[14] Outdoor patient(OPD) services began at the AIIMS Jodhpur from 27 July 2013.[15] AIIMS has started MD courses in Anatomy, Biochemistry, Physiology and Community Medicine and Family Medicine departments from 2016.[citation needed] AIIMS Jodhpur started Postgraduate courses in 20 departments from 2017 with 56 seats.[16] Admissions to the post graduate courses is done through a common entrance exam known as Institute of National Importance-Common Entrance Test (INI-CET) along with PGI, Chandigarh, JIPMER Puduchery, NIMHANS Bangalore and SCTIMS, Trivandrum. AIIMS Jodhpur admits 194 PG students every year. The institute also admits students in superspeciality (DM/MCH) program through INI-SS Exams conducted by AIIMS Delhi.[17] AIIMS Jodhpur uses innovations in Medical Education and patient care. AIIMS Jodhpur Model of Medical Education utilizes Unconventional Learning Experiences (UNCLE) for delivering Competency Based Medical Education in its special sessions on Saturdays. The President of India, Shri Ram Nath Kovind graced and addressed the students during 2nd Convocation of the institute on 7 December 2019 and lauded the efforts of AIIMS Jodhpur in collaborating with IIT Jodhpur for medical innovation course [18][19]