The fire was reported around 5 p.m. at the facility located by Sepulveda Boulevard and Alameda Street.
Thursday's fire was smaller than a blaze at the same facility on March 15 that shut down an entire unit. This fire was contained to a single room.
Firefighter crews from the refinery were joined by L.A. County and other agencies in battling the flames.
Firefighters say some residual oil in a mechanical pump caught fire.
People in nearby cities were advised to keep windows closed as the flames emit thick clouds of smoke into the air.
But firefighters later said air quality testing showed no serious concerns for toxic materials in the air.
It's not clear if the refinery fire will affect production enough to cause a spike in gas prices. The answer to that question will be more apparent after energy markets open Friday morning.