Novaturas said on Wednesday it would not operate flights to Bulgaria between July 9 and July 31.
"Travelers' safety is our top priority," it said in a statement.
The company will carry out return flights scheduled for the near future to fly home travelers who are currently in Bulgaria.
Those whose trips are cancelled due to the pandemic are advised to rebook to a safe resort in Greek, move their trips to a later date or opt for vouchers.
Tez Tour said on Wednesday it was cancelling trips to Bulgaria for July 9 through 31, offering travelers to fly to Greek resorts instead.
"We are canceling trips to Bulgaria to keep our travelers safe," the company said in a statement.
Lithuania currently offers charter flights to Bulgaria and Greece, and regular flights to Croatia and Cyprus.
Milda Plepyte-Rainiene, the managing director of the Lithuanian Tourism Association, said all of the first post-quarantine flights to Greece and Bulgaria had been fully booked.
Health Minister Aurelijus Veryga on Wednesday added Bulgaria, Romania and several other countries to the list of COVID-19 affected countries.
Lithuanian residents and foreigners who hold a permit to enter Lithuania must spend two weeks in self-isolation if they return to Lithuania from a country on the list.