There will be four weekly flights on Mondays, Wednesdays, Fridays, and Sundays, the Vietnamese budget carrier says on its website.
Currently people flying on the route have to transit in HCMC.
Both Vietnam and Thailand have reopened their borders to foreign tourists and lifted most Covid restrictions.
The Thai government will increase from October the period of visa-free stay for tourists from over 50 countries, including Vietnam, from 30 days to 45.
Phu Quoc, Vietnam's largest island, is famous for its white-sand beaches and fish sauce, an indispensable Vietnamese condiment.
The island has become globally popular since the government allowed 30-day visa free entry in 2014.