The station is operated by Pertamina, Indonesia’s state-run energy company.
Social media footage showed a huge flame billowing and people running for cover.
Some nearby residents have been evacuated and Jakarta’s firefighting force has dispatched 52 units to respond to the blaze.
Pertamina will investigate the cause of the fire and provide treatment for those affected, the company’s CEO Nicke Widyawati told CNN Indonesia.
Fuel supplies for Jakarta will be provided from other terminals nearby, Widyawati said.
In 2018, an oil spill cause by a leak of Pertamina’s undersea crude pipelines killed five fishermen.
Indonesian authorities at the time declared a state of “emergency response” over the massive scale of the spill and environmental damage off the coast of the Southeast Asian country.