Thirty-five fishermen and one civilian were released after they completed their sentences, Dawn online reported.
The prisoners will be repatriated to India through the Wagah border check post near Lahore.
The prisoners said they were very happy to be released and could not wait to be reunited with their loved ones.
They also said they were treated fairly in Pakistan.
At least 419 Indian fishermen are currently held in Karachi's district prison Malir.
Such arrests are frequently carried out by both countries, as the maritime border in the Arabian Sea is poorly defined and many fishing boats lack the technology needed to be certain of their precise location.
The fishermen often languish in jail even after serving their term, as poor diplomatic ties between the two arch rivals mean fulfilling official requirements can take a long time.