The release is part of an understanding between the two countries 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 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 Sindh, 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.
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