The Tezpur base is one of the premier forward fighter bases of the Indian Air Force in the eastern sector.
Rathore replaces Air Commodore Sandeep Singh, a defence release said here.
Prior to his new appointment, he was on deputation to Israel as Air Attache.
Rathore was commissioned as a fighter pilot in 1986 and is a graduate of Defence Services Staff College. He is also a qualified flying instructor.
He held many important appointments in his career including as Commanding Officer of 20 Squadron of IAF, the release added.