Pakistan opened the border on Tuesday for two days at Torkham in Khyber tribal region and Chaman in Balochistan province which are the most popular routes to travel to Afghanistan.
Over 32,000 Afghans and 2,700 Pakistanis crossed into their respective countries via the Torkham and Chaman crossing points yesterday, the last day of reopening of the border, Dawn reported.
"In two days, over 51,000 Afghans and 4,900 Pakistanis returned to their respective countries after the Pakistan government reopened the border crossings on Tuesday," the report said.
Female paramilitary Frontier Corps (FC) personnel were also deputed at the border to help guide returning Afghan women and their children.
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According to officials, 11,500 Afghans crossed the border yesterday and 12,539 on Tuesday. About 700 Pakistanis returned home in two days.
The Afghans waiting in long queues at the Torkham crossing expressed mixed feelings about reopening of the border and their return journey.
According to officials, 20,870 Afghans crossed into their country, while 2,631 Pakistanis returned home via the Chaman border crossing. In two days, 27,718 Afghans went back to Afghanistan and 4,277 Pakistanis returned to Chaman.
The border was again closed indefinitely.
"We have closed the border again for an indefinite period," a senior security official said, adding that he was not aware when it would reopen.
The two countries have long accused each other of failing to combat extremists who operate along their porous frontier.