Between 8,000 and 10,000 people flocked into Afghanistan via Torkham on Tuesday, officials said.
The crossing was reopened for four days on Monday.
On the first day, Afghan authorities received 1,000 nationals carrying legal travel documents and refused entry to the remaining on the pretext that they had a capacity of 1000 coronavirus suspects at their quarantine centre.
Rahat Gul Ziarmal, the mayor of Torkham, said on the second day, people crossed without authorities having their passports stamped for exit and entry.
Pakistan has registered more than 4,000 coronavirus cases while Afghanistan has 423 confirmed cases.
