The budget carrier began to serve the routes from Incheon International Airport to the two Asian cities on Thursday, the company said in a statement.
Local airlines have suspended or reduced flights on routes to some less-popular Japanese cities since August amid a trade row between South Korea and Japan.
To protest Japan's curbs on exports of some industrial materials to South Korea, Koreans here have shunned traveling to the neighboring country.
Jeju Air shifted to a net loss of 30.1 billion won ($27 million) for the July-September quarter from a net profit of 31.1 billion won a year earlier.
South Korean travelers increasingly opted not to travel to Japan due to Japan's export curbs, dealing a blow to the quarterly earnings results. The won's weakness against the US dollar also weighed on the bottom line, the company said.
The airline operates 45 B737-800s -- 42 chartered and three purchased. The planes serve six domestic routes and 70 international routes, mainly to Singapore and other Southeast Asian countries. (Yonhap)