A hydrogen filling system includes a first tank and a second tank that are configured to be filled with hydrogen and communicate with each other, a first hydrogen feeder and a second hydrogen feeder configured to feed hydrogen to the first tank and the second tank, and a controller configured to control the first hydrogen feeder and the second hydrogen feeder. The controller estimates a hydrogen fill factor of the first tank and the second tank, based on a first internal temperature of the first tank and a second internal temperature of the second tank, and a first pressure of hydrogen gas fed from the first hydrogen feeder and a second pressure of hydrogen gas fed from the second hydrogen feeder. The controller is configured to stop the first hydrogen feeder and the second hydrogen feeder when the hydrogen fill factor reaches a predetermined threshold fill factor.