The team will be given access to all the witnesses to the attack, but  the Press Trust of India news agency said they would not be able to interview security personnel.
India accused Pakistan-based group Jaish-e-Mohammad of carrying out the assault in January.
Seven Indian soldiers and six militants were killed in the attack.
This is the first time that Pakistani intelligence and police officials have travelled to India to investigate a militant attack.
The Pakistan team's visit came after Indian Foreign Minister Sushma Swaraj met Pakistan's foreign affairs adviser Sartaj Aziz on the sidelines of a regional meeting in Nepal.
In February, police in Pakistan registered a complaint against "unknown persons" over the Pathankot attack.
An official of the interior ministry of Pakistan had filed the complaint, which mentioned some Pakistani mobile numbers provided by Indian authorities.
The United Jihad Council (UJC) - a coalition of more than a dozen militant groups fighting against Indian rule in Kashmir - said they carried out the attack.
The claim was met with scepticism - the UJC's core members are not known to have carried out attacks outside Indian-administered Kashmir.
Indian security officials instead blamed Jaish-e-Mohammed.
Started by Masood Azhar, the Islamist militant group has been blamed for attacks on Indian soil in the past, including one in 2001 on the Indian parliament which took the nuclear-armed rivals to the brink of war.
A five-member team from Pakistan is in India to investigate a deadly militant attack on an air force base.