The release comes two weeks after Indian Prime Minister Manmohan Singh and his Pakistani counterpart Yousaf Raza Gilani watched side by side as India beat Pakistan in the cricket World Cup semi-final in northwest India.
"Today we released 89 Indian fishermen from Malir prison as a goodwill gesture," prisons chief Ghulam Qadir Thebo told AFP.
These fishermen were caught during the past 13-19 months fishing in Pakistani territorial waters, he said.
Two buses set off for the eastern city of Lahore, where they will cross the Pakistan-India border on Friday, he added.
Pakistan and India frequently seize each other's fishermen, accusing them of violating their respective zones in the Arabian Sea.
The Pakistani foreign ministry said India had handed over a list of prisoners during the talks between home secretaries in New Delhi last month.
"The Indian side has handed over 39 Pakistani prisoners on 11 April from the list that Pakistan had given to India," it said in a statement.
Pakistan last week released a jailed Indian, Gopal Das, who had been held for 23 years.
The move was seen as another confidence-building measure as India and Pakistan look to get their stalled peace process back on track.
Peace talks between the two rivals, started in 2004, were derailed after gunmen -- who India insists came from Pakistan -- staged bloody attacks in Mumbai which left 166 people dead in 2008.
Gilani became the most senior Pakistani leader to visit India since 2001 when he watched the cricket semi-final late last month with Singh.
Pakistan and India, who have fought three wars since the division of the subcontinent in 1947, have agreed to a series of high-level talks until July to shore up the fragile detente.
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