The majority of the refugees crossed in July and August, Qaisar Khan Afridi, spokesman UNHCR at the Voluntary Repatriation Centre outside the north-western city of Peshawar, near the Afghan border said.
In the six months prior to that just 7,000 refugees crossed back into Afghanistan, according to UNHCR figures.
Pakistani officials said the increase came after they vowed to tighten border controls, particularly at the porous Torkham Gate crossing.
However UNHCR cited an array of other reasons that could be helping drive the rush back into war-torn Afghanistan, including increasing anxiety and insecurity for refugees about life in Pakistan.
Pakistan is home to 1.5 million registered and about as many undocumented Afghan refugees, with growing insecurity in Afghanistan impeding voluntary return programmes.
But UNHCR said refugees are increasingly anxious about their future in Pakistan.
In June, Islamabad granted Afghan refugees an extra six months to remain in Pakistan as authorities stepped up efforts to work with the UN and Kabul to relocate camps to Afghanistan. Fears are growing that the December deadline will be final.
A security crackdown against undocumented foreigners has also contributed to the decision to leave, despite assurances from Pakistani authorities that refugees with the correct documents will not be subject to arrest or deportation.
Other factors include the UNHCR decision to double its cash grant for voluntary returnees from $200 to $400 per individual in June, and a campaign by the Afghan government to lure its citizens back with the slogan “My country, my beautiful country”.
In Peshawar thousands of men, women and children waited for their turn for verification at UNHCR’s Voluntary Repatriation Centre in the suburbs of Peshawar this week.
Afridi said they expect even more after the religious feast of Eid al-Adha next week, adding that UNHCR plans to open another repatriation centre in Peshawar to cope.
The vast majority of those returning had been living in Pakistan’s north-western Khyber Pakhtunkhwa province, of which Peshawar is the capital.
The rest were repatriated from south-western Balochistan province.