The popular Friendship Express arrived in the border station of Attari from the Pakistani city of Lahore. The first train was only partially full, with a little over 60 passengers, the BBC reported.
Earlier the Samjhauta Express, with freshly painted green and yellow coaches decorated with bunting, crossed the border between India and Pakistan before proceeding to Attari.
The two countries broke off most ties in 2001 after India blamed Pakistan for involvement in an armed attack on the federal parliament in Delhi. Relations have improved recently and bus and air links have been restored.
Wednesday, India and Pakistan agreed to continue a bus service linking Lahore with Delhi for another five years. The bus service was launched in 1999 after Indian Prime Minister Atal Behari Vajpayee traveled to Lahore for talks with then-Pakistani Premier Nawaz Sharif.