PM met the girl at his official residence at 7RCR and even shared his picture on social media.
"Truly wonderful to have you (Geeta) back home. Was truly a delight to spend time with you today," PM tweeted.
The PM also lauded the efforts of Edhi family in Pakistan for taking care of the girl.
"Don't think any amount of words are enough to thank Edhi family for taking care of Geeta. They are apostles of kindness, compassion," he further tweeted.
The PM has also announced an aid of Rs 1 crore to the Edhi family's foundation.
What the Edhi family has done is too priceless to be measured but I am happy to announce a contribution of Rs. 1 crore to their foundation.— Narendra Modi (@narendramodi) October 26, 2015
Earlier in the day, Geeta returned to India but could not recognise the family she had earlier identified from photographs even as the government "whole- heartedly" thanked Islamabad for allowing her homecoming.
External Affairs Minister Sushma Swaraj called it a "happy day" after meeting Geeta as the "innocent daughter came back home".
She said the government will do everything possible to reunite her with her family.
The Mahato family from Bihar, which claimed Geeta to be their daughter, met her in presence of Swaraj, but she refused to recognise them though she had identified them from photographs when she was in Karachi. [Sushma thanks Pakistan after Geeta's return]
"I am very happy to be in India. My heart is filled with happiness. I am touched the way I am being welcomed. In Pakistan, I used to often feel sad," said Geeta, through a sign language interpretor, at a press conference along with Swaraj.
Dressed in a red and white salwar kameez, Geeta, who had accidentally strayed into Pakistan 14 years back, said her priority is to stand on her feet and that she did not have plans for marriage.
Swaraj said Geeta will stay in a rehabilitation centre for deaf and dumb people in Indore and that she will be imparted skill development training there.
"I thank the Edhi foundation which took care of her all these years. I on behalf of people of India and government thank Pakistan government for facilitating Geeta's return... It is a happy day for us innocent Geeta came after so many years," said Swaraj.
She, however, refused to answer questions on whether Geeta's homecoming will help improve relations between India and Pakistan.
Geeta was adopted by the Edhi Foundation's Bilquees Edhi and lived with her in Karachi.
Bilquis and her grandchildren, Saba and Saad Edhi, have accompanied Geeta here.
Swaraj hailed Edhi foundation for respecting Geeta's religious faith and bringing idols of various Gods for her.
(With inputs from agencies)