The 99 Indian prisoners, including 96 fishermen, who were freed from Pakistan jails on Friday, were handed over to Indian authorities at Wagah border on Saturday.
All of them were issued emergency travel certificates by the Indian High Commission in Islamabad.
Three prisoners were identified as Parvez Ahmed from Kashmir, Mangal Singh from Jammu and Shabudin from Poonch.
Parvez was arrested in 1992, while Mangal Singh was arrested in 1997 and Shabudin was arrested in 1991.
On reaching the Indian soil, most of the prisoners thanked the Indian government for its efforts to hold talks with the Pakistan government to get them released.
The Pakistan government freed them as a goodwill gesture close on the heels of External Affairs Minister Pranab Mukherjee's visit to that country.
The move came two days after India and Pakistan signed an agreement, about granting consular access to each other's citizens, being held in the jails of the two countries.
Indian authorities had earlier confirmed the nationality of the fishermen and other prisoners.
The fishermen were arrested after they strayed into Pakistan's territorial waters.
Hundreds of fishermen from both countries are arrested every year by India's Coast Guard and Pakistan's Maritime Security Agency for accidentally drifting into each other's territorial waters.