Flight VN426 departed from Hanoi with 148 passengers on board, and another run by the national flag carrier returned from Busan with 175 passengers.
The airline is operating three flights per week on the route every Monday, Tuesday and Friday.
As from July, it will also reopen the Ho Chi Minh City-Busan route with four flights per week, and plans to launch flights connecting Hanoi, HCM City, Da Nang and Nha Trang with Seoul.
Wide-body Boeing 787 aircraft will be used on the routes.
Tickets are available at www.vietnamairlines.com, booking offices and sale agents of Vietnam Airlines nationwide.
Budget carrier Vietjet Air on June 3 also welcomed passengers back on its journey between Ho Chi Minh City of Vietnam and Phuket, a popular tourist destination of Thailand.
The airline, the first in Vietnam to resume flights between the two localities, will operate four round trips on Mondays, Wednesdays, Fridays and Sundays, each lasting two hours.
Vietjet earlier resumed flights from HCM City, Hanoi and Da Nang to the Thai capital city of Bangkok. The airline now has the biggest number of routes between Vietnam and Thailand.