The release is part of an understanding between the nuclear-armed rivals to free citizens who mistakenly stray into each other`s waters.
"Some 55 Indian fishermen have been released from our jail on the instructions of the government," said Nazeer Husain Shah, superintendent of Malir district prison in Karachi.
"Those released include 15 teenage boys," he told AFP.
The Indians were presented with flowers and gifts, then bused to the eastern city of Lahore, from where they would cross the Wagah border.
Officials say 100 Indian fishermen are still in Pakistani jails and 250 Pakistanis in Indian prisons.
Ayaz Soomro, law minister for the southern province of Sindh on the Arabian Sea, said the releases were "a goodwill gesture".
"We hope our neighbours reciprocate in the same spirit and release Pakistani prisoners from their jails," he said.
India and Pakistan have fought three wars since independence in 1947, two of them over the Himalayan region of Kashmir, which is divided by a heavily militarised Line of Control and which both countries claim in full.
Last year they resumed their tentative peace process, which collapsed after Islamist gunmen from Pakistan killed 166 people in Mumbai in November 2008.