Police said the attack happened at 1.45am on the Ban Pa Thung-Ban Bang Kao Road in Tambon Bang Kao's Moo 4 village.
The car was being driven by Solahuddin Haware, 40, a resident of Pattani's Sai Buri district.
The girl, Nura-afika Tahe, was standing on the back passenger compartment clinging to the two front seats.
Police said two insurgents on a motorcycle caught up with the car and the pillion rider opened fire. The bullet went through the right back window and hit the girl's right arm.
She was taken to the Sai Buri district hospital.