The private carrier began operating a daily return flight with an MD-82 aircraft on Tuesday, said a company employee at Jakarta's Sukarno-Hatta international airport.
"The plan is to gradually raise the frequency to four return flights a day but we do not have the precise schedule yet," the employee said.
Lion Air charges 121 dollars including tax for the return trip and says this is about 33 percent lower than other airlines.
It will compete head-on with Singapore Airlines and Garuda Indonesia for business on the route, one of the region's busiest.
Lion Air was established in 2000. It currently serves 32 domestic routes plus Kuala Lumpur and Singapore.