Iftikhar Ahmad was received by Pakistani officials on the main border between the neighbouring regions on Saturday.
His father, Gulzar Ahmad Tantray, took him to India last year on the pretext of attending a wedding.
Pakistan has thanked India for returning Iftikhar.
"I had lost all hope of getting my child back," Iftikhar's mother Rohina Kayani told reporters, describing it as a "miracle".
"I am thankful to the Pakistani government for its help," she said.
Ms Kayani lives in Pakistani-administered Kashmir, while Mr Tantray now lives in
Indian-administered Kashmir.
Iftikhar became the centre of a controversy between India and Pakistan when Mr Tantray was arrested in March 2016.
Mr Tantray, who grew up in a village in Ganderbal, crossed over to Pakistan-administered Kashmir in 1990, allegedly for arms training at the peak of the insurgency against Indian rule.
He returned to India-administered Kashmir with Iftikhar, where he was taken into police custody.
At the time, Rohina Kayani accused her husband of abducting the child and running away to the Indian side. Mr Tantray and his family have denied charges of kidnapping.