Officials said that of the 14-hour journey of 500km, around six hours would be needed for completing customs and immigration formalities at the border stations in Bangladesh and in India.
Due to security concerns, Monday's journey reportedly took 12 hours.
Officials also say that the train would make the trip twice a week, but its frequency would be raised.
"It's a historic occasion for both the countries. We will be more closer after the resumption of the India-Bangladesh passenger train service," Iftekhar Ahmed Chowdhury, Bangladesh's foreign minister, said.
In India, his counterpart Pranab Mukherjee flagged off the Maitree [Friendship] Express from Kolkata with 65 passengers on board on the first day of the Bengali New Year.
Al Jazeera's Hannah Belcher, reporting from Dhaka, said that the resumption of transport links took a very long time.
"Bangladesh and India signed a deal in 2001, to resume a direct train service," she said.
"But the service has been delayed by India's insistence on the construction of a 150m security cage along the railway passage, built in an attempt to stop smuggling and illegal immigration."
Belcher also said that there were efforts to stop this occasion from going ahead.
Passenger services between the two countries were suspended after a war between India and Pakistan in 1965.
Bangladesh, formerly East Pakistan, severed ties with Islamabad and gained indepence in 1971 with the help of the Indian military.
The area of Bengal was partitioned along religious lines in 1947 when the subcontinent gained independence from British colonial rule.
Thousands of people on both sides of the India-Bangladesh border have relatives on the other side and speak the same language, Bengali.