There will be three weekly flights on Mondays, Wednesdays and Sundays.
Vietnam Airlines is the first Vietnamese carrier to reopen regular commercial flights with Hong Kong, Ngo Tri Hung, chief of the airline's branch in Hong Kong, said as quoted by Vietnam News Agency.
The airline will consider increasing the frequency of flights between the two destinations in the coming time, he added.
Vietnam is currently the eighth largest trade partner of Hong Kong while Hong Kong is the fifth largest investor in the country.
The Hong Kong-Hanoi route was suspended in February 2020 due to Covid outbreak.
On Friday, the national flag carrier also resumed air service to China after nearly three years.