The JAC called the bandh to protest the Centre's flip-flop over the creation of Telangana state.
Several long-distance trains, including the Secunderabad-New Delhi AP Express, were delayed by many hours as the agitators were holding 'Rail Roko' programmes at Secunderabad and other stations.
However, parts of old Hyderabad, which has a sizeable Muslim population, remained unaffected by the bandh.
The administration has also declared holidays for educational institutions including private schools in Hyderabad and other places.