Iizaka Onsen Station has two bay platforms serving a single bi-directional track.

The ground-level floor of the building contains a FamilyMart convenience store, a small vegetable shop, and a Fukushima Shinkin Bank ATM.

The basement level contains the ticket gate and platforms, the station office, the waiting room, and toilets.

From 1908 to 1967, Fukushima Kōtsū Iizaka East Line's Yuno-machi Station (湯野町駅) was a five-minute walk away, but it was shut down when the Iizaka East line closed.

Iizaka Onsen Station's building was renovated in 2010, and the new look was revealed on December 20, 2010.