Gupta, who is presently holding the additional charge of the post, has been appointed for five-year term, an order issued by Department of Personnel and Training said.
He is presently working as Director (Operations and Commercial) in the Konkan Railway.
The 741-kilometre Konkan Railway line connects Maharashtra, Goa and Karnataka.
In another order, the Centre has extended the additional charge of Managing Director, HMT Watches Ltd, given to B M Shivashankar for six months beyond May 1, 2016.
Shivashankar is presently Director (Technology), HMT Machine Tools Ltd.