The regime is expected to also release 1,500 detainees under the deal, and allow food aids to enter the besieged towns Madaya and Zabadani in Rural Damascus.
Meanwhile an evacuation is expected to take place Wednesday morning, with some 1,000 people leaving the town of Madaya and 150 others leaving the town of Zabadani, to be taken to the Idlib province.
An unknown number of people will be evacuated from pro-regime towns of Foua and Kefraya, heading for the city of Aleppo.
The Syrian regime struck a number of deals with local rebels, under which they evacuate for rebel-held parts of northern Syria, bordering Turkey.
Many have criticised the deals, calling it a deliberate policy of demographic change to forcibly displace Bashar al-Assad's opponents away from the main cities of western Syria.
Thousands of rebel fighters and their families were evacuated to the Idlib province as thousands of people from the Shia towns of Foua and Kefraya headed to regime-held parts of Aleppo.
People from the four towns registered their names to leave and combatants began opening up the roads, Reuters reported, citing the Syrian Observatory for Human Rights.
The Observatory said the evacuations were the biggest population swap agreement, but Observatory director Rami Abdel-Rahman described the agreement as "demographic change on sectarian basis".