Since 1 April at least 44,900 people have returned, with around 58% of them children, according to the UN Refugee Agency (UNHCR).
At least 8,906 Afghan nationals have been deported since April 1, the UNHCR said in a WhatsApp message.
Pakistani authorities closed the border to vehicles coming in from Afghanistan after the scanning machine used to track imports developed technical problems.
The reopening follows successful diplomatic talks between jirga officials from both countries.
The Pakistani authorities have requested that the Islamic Emirate of Afghanistan (IEA) refrain from constructing new facilities along the Durand Line.
Custom officials and clearing agents also stayed back while goods clearance was also halted on Saturday.
The busy border crossing was closed for all trade and travel and Afghans were advised by the Islamic Emirate to avoid using this route.
Islamabad banned the export of sugar to Afghanistan four years ago to address shortages and control prices in the country.
Meanwhile, Nangarhar officials said they are trying to solve these problems through dialogue with Pakistan.
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