The men were executed at jails in Karachi and Hyderabad.
They hijacked a Pakistan International Airlines flight in May 1998 and ordered the pilot to fly to India but the plane was diverted and stormed by troops.
Pakistan has put at least 130 people to death since lifting a moratorium on executions in December.
The men - Shabbir Rind, Shahsawar Baloch and Sabir Rind - were members of the left-wing Baloch Students' Organisation (BSO), who were demanding more resources, such as gas and electricity, for their region.
They were sentenced to be executed in October 1998 but remained on death row until a moratorium on executions was lifted after the Peshawar school massacre.
Four other men were hanged on Thursday at jails across the country. They were convicted in murder cases and were not linked to the hijackers.
PIA flight 554 took off from Turbat, in the south of Balochistan, and was heading for Karachi when the attackers boarded during a stop-over in Gwadar.
They commandeered the Fokker shortly after take-off, and demanded the captain fly directly to Delhi.
He told them there was not enough fuel, but agreed to bring the plane as far as Bhuj, an airstrip in Gujrat, India.
Instead, he landed in Hyderabad where security forces were waiting.
BBC Urdu's Riaz Sohail in Karachi reports that in order to let the hijackers think they were in India, authorities banned the use of loudspeakers in mosques around the airport.
Troops then stormed the plane and overpowered the hijackers. Passengers and crew were unharmed.
The hijacking on 24 May came just four days before Pakistan carried out nuclear tests in Balochistan, which the BSO opposed.
The province is one of the most underdeveloped regions in the country and has become the site of a long-running conflict between separatists and security forces.
Pakistan has hanged three Baloch insurgents, 17 years after they hijacked a passenger plane with 30 people on board.