The express was not allowed to cross the border for the past week. The authorities had turned the express back twice in the last week due to ongoing protests by farmers in Punjab.
The total 192 passengers, including 122 Indians and 72 Pakistanis, are travelling in the train.
The Indian railways informed Pakistani authorities concerned that the train is vulnerable to attacks on its way as agitated farmers have resorted to protests.
As many as 86 Indian nationals had crossed Wagah-Attari border on foot on Tuesday.