The arrests came after Pakistan supplied information to the Afghan government.
Afghan officials denied reports that the five had been handed over to Pakistan, saying they would be questioned in Afghanistan first.
Taliban gunmen killed at least 150 people, mostly children, in the attack.
An Afghan security official said the five had been arrested in an eastern province.
The arrests confirm there has been a recent thaw in relations between the Afghan and Pakistani governments, the BBC's David Loyn reports from Kabul.
Afghan President Ashraf Ghani made a successful trip to Pakistan soon after coming into office last October and both sides have promised better cross-border co-operation.
Afghan security officials believe the five arrested were indirectly involved in the school massacre on 16 December. All seven gunmen were killed.
They had cut through a wire fence to gain entry to the Army Public School and then went from class to class, killing at least 150 people - 133 of them children - and injuring more than 120.
The Taliban said the attack was in response to a government offensive in North Waziristan and the nearby Khyber area that began in June 2014.
The killings were condemned across the world and the Afghan Taliban also criticised them.
This week pupils and teachers returned to the school for the first time since the attack.
In another development, the leader of Pakistan's opposition PTI party, Imran Khan, was barracked by parents of the victims on a visit to the Peshawar school.
A small group of parents blocked his motorcade and shouted slogans accusing him of failing to show real concern.
The PTI initially accused rival political parties of engineering the protest but the other parties denied any involvement and correspondents said the outburst appeared to be an expression of genuine anger.
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