The service, four times a week, was launched recently with an inaugural flight by the airline's new ATR72-500 turboprop aircraft.
"We can now expect many first-time leisure travelers to Koh Samui from Kuala Lumpur, now that we are connecting the capital of Malaysia directly through this route," Firefly head of communications and marketing Angelina Fernandez said.
"More people will be able to experience what Koh Samui has to offer. We are also honored to be able to encourage the people of Thailand to visit Kuala Lumpur and Malaysia," the New Straits Times quoted Fernandez as saying.
This new route would enable expatriates living in Malaysia to do their "visa runs" and at the same time take the opportunity to explore Malaysia via the new route, she said.
"We expect Koh Samui to be one of our top Thailand destinations and we are happy to provide the service, which is why we have holiday packages via Firefly Holidays," she said.
Firefly Holidays packages start from as low as 180 ringgit (51 U.S. dollars) per person to 2,800 ringgit (795 U.S. dollars) for a three day, two night stay.