JR-Fujinomori Station has two separate platforms and two tracks; the station building's functional center is on the second floor, and the station building and the track sit on the site created by digging out the ground, so the platforms can be seen from the ground level from outside the station.
相対式2面2線プラットホームを持つ地上駅で、掘り割り型の橋上駅舎である。