Iftikhar Ahmed, a 5 year-old Pakistani boy was apparently "forcibly" taken to India by his father a year ago.
After pangs of separation, her mother filed a case in an Indian court for his custody.
India repatriated two Pakistani nationals, including five-year-old Iftikhar Ahmad, from Attari border on Saturday. He took the boy to Dubai and then to Ganderbal.
The child was to be handed over to his mother in Pakistan in May 2016.
On Saturday evening, Iftikhar was finally reunited with her mother and other relatives, who were present at the Wagah border to receive him.
Pakistani high commission said it was victory of the high commission to get the child returned to his homeland. The boy was handed over to her mother by Pakistani Rangers.
"I had lost all hope of getting my child back", Iftikhar's mother Rohina Kayani told reporters, describing it as a "miracle".
Ms Rohina said that she had no objection to her husband's meeting with their child and she was even ready to live with him (her husband) if he wanted.
Compliance with the Indian high court's orders took over nine months due to India-Pakistan border tensions and the lengthy clerical procedure involved for handing over a person to Pakistan.
She thanked the prime minster of Pakistan, Punjab chief minister, Interior Ministry and Pakistani High Commissioner to India Abdul Basit for their cooperation.