IIT Jodhpur was first announced by the Central Government in July 2007, although the formal announcement was made in 2008, with IIT Kanpur mentoring IIT Jodhpur. In July 2008, the first academic session of IIT Jodhpur began at the IIT Kanpur campus, with 109 undergraduate students in Computer Science Engineering, Mechanical Engineering, and Electrical Engineering. The institute was sanctioned as an IIT for Rajasthan, and not for Jodhpur in specific. It was after considering various cities, including Ajmer, Bikaner, Jaipur, Jodhpur, Kota, and Udaipur that Prof. Vijay Shankar Vyas led the committee to suggested Jodhpur as the location for the IIT in Rajasthan. In late 2009, the MHRD granted final approval for establishing the institute at Jodhpur.

A portion of the MBM Engineering College under JNV University, Jodhpur was identified as the location for the transit campus of IIT Jodhpur. In May 2010, classes of IIT Jodhpur were shifted from IIT Kanpur to the transit campus in Jodhpur. In July 2017, the academic and residential campuses of IIT Jodhpur were migrated to the permanent campus. Construction of the permanent campus is still in progress.

IITJ has located about 24 km from Jodhpur city on National Highway 62 which connects Jodhpur to Nagaur. The site spans over 852 acres (3.45 km2) of land around Jhipasni and Gharao villages. M. M. Pallam Raju, then Union Minister for Human Resources Development, laid the foundation stone on 16 April 2013.

The permanent campus is being built on a self-sustainable model, catering to its own energy and water requirements. The campus' masterplan got 'GRIHA Exemplary Performance Award' under the 'Passive Architecture Design' category at the 8th GRIHA Summit held during 2–3 March 2017, at India Habitat Centre, New Delhi.
Source: https://en.wikipedia.org/wiki/IIT_Jodhpur