Arrested by the Federal Bureau of Investigation in October, Headley has been charged with criminal conspiring in the 26/11 Mumbai terror attacks that claimed 166 lives.
Rana, who has also been denied bail, faces charges that he provided support to Headley in plotting attacks against a Danish newspaper.
Headley in particular made several trips to India to secretly capture videos and photographs on behalf of the Lashkar-e-Tayiba of the prospective targets of their attacks in India.
Authoritative sources told PTI that the Indian visa of Rana and Headley along with two others were cancelled a day after the FBI filed the case against them in a Chicago court.
Besides Headley and Rana, Indian visas have also been cancelled of those of Rana's wife Samraz Rana Akhthar and his business partner Raymond sanders.
A circular in this regard has been issued to all the overseas Indian missions and point of entry in India. The United States too has been informed about it so does the individuals whose visas have been cancelled.
While Headley was issued a five-year multi-entry business visa in July 2007, Rana was given a one-year business visa, valid up to March 2011, and both were also exempted from police reporting if their stay was less than 180 days at a single stretch.