The Maritime Security Agency (MSA) made the arrests Saturday night, and also impounded 19 wooden boats, a security official said.
"The 100 men would be taken to the court on Monday," senior police official Adeel Chandio said after the fishermen were handed over to the police by MSA officials.
Every year dozens of Indian and Pakistani fishermen are picked up in the Arabian Sea after straying across maritime borders.
India releases 39 Pakistani prisoners as goodwill gesture
They often languish in prison even after serving their sentences, as poor diplomatic relations between the bitter nuclear foes hamper the bureaucracy.
Pakistan released 219 Indian fishermen as a "goodwill" gesture in January.
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