The released prisoners were taken to the Karachi Cantonment Railway Station under heavy security, where they boarded the Allama Iqbal Express for Lahore, The Express Tribune reported.
From Lahore, they would be taken to the Wagah Border for handover to the Indian authorities, it said.
The prisoners were arrested for trespassing into the country's territorial waters and violating international maritime limits.
They were given gifts and provided travel expenses by the Edhi Foundation, a non-profit social welfare organisation in Pakistan, the report said.
On Friday, Pakistan announced that it will release 360 Indian prisoners, mostly fishermen, this month in four phases, as a "goodwill gesture".
Foreign Office spokesperson Mohammad Faisal said the process of releasing the Indian fishermen will start on April 8 when 100 prisoners will be released.
Another 100 will be released in the second phase on April 15 and in the third phase on April 22, another 100 will be set free. The fourth and last phase on April 29 will see the release of the remaining 60 prisoners.
"We are doing it as a goodwill gesture and hope that India will reciprocate it," Faisal said while addressing his weekly briefing to the media in Islamabad on Friday.
Currently, there are 347 Pakistani prisoners in India and 537 Indian prisoners in Pakistan, he said.
"Pakistan will release 360 Indian prisoners, of which 355 are fishermen and five are civilians," Faisal said.
Anwar Kazmi, a spokesman of Edhi welfare organisation which helps the released fishermen with clothes and food, told PTI from Karachi on Friday that the process of releasing the fishermen will start from Sunday.
"First a group of 100 fishermen will be taken from Karachi to Lahore on Allama Iqbal Express on Sunday," he said.
They are likely to be handed over to India on Monday at Wagah. They spent months and sometimes years before repatriated.
Pakistan and India frequently arrest fishermen as there is no clear demarcation of the maritime border in the Arabian Sea and these fishermen do not have boats equipped with the technology to know their precise location.
Owing to the lengthy and slow bureaucratic and legal procedures, the fishermen usually remain in jail for several months and sometimes years.
Pakistan's announcement to release the fishermen came amidst escalating tensions between India and Pakistan after a suicide bomber of Pakistan-based Jaish-e-Mohammed (JeM) terror group killed 40 CRPF personnel in Jammu and Kashmir's Pulwama district on February 14.
India launched a counter-terror operation against a JeM training camp in Balakot in Pakistan's Khyber Pakhtunkhwa province.