The formation of lava tubes is one of the most significant factors controlling the emplacement of lava flows. However, extents and structures of lava tubes are typically not precisely known due to the difficulty in finding lava tubes in the field. We developed a new stepped-frequency ground penetrating radar (GPR) system with shielded antennas, which allows measurements that have both high spatial resolution and large penetration depth. We performed two types of measurements over an inactive lava flow and show that this method can easily detect the existence of a lava tube. Importantly, phase reversals of the reflection signals can help identify reflections from a lava tube. Using these reflection patterns, we estimate the vertical dimension and the depth of a lava tube at Fuji volcano, which are validated by survey measurements. The presented method may be the most practical way to map terrestrial and perhaps extraterrestrial lava tubes.