Although Tokyo daruma pond frogs (Pelophylax porosus porosus) were once commonly observed throughout paddy fields in Japan, their populations have recently declined. The mode by which frogs survive during the overwintering period is largely unknown. In this study, we observed the underground behavior of 12 free-living Tokyo daruma pond frogs that overwintered in paddy soil and a dry field by periodically excavating their overwintering positions from late March to early May. The mean overwintering depth of these frogs was ~19.8 cm, with 10 having migrated toward the soil surface (mean depth: ~8.6 cm) by late March, and finally, all 11 live frogs migrated further upward close to the soil surface. In addition, males tended to emerge earlier in spring than females. One monitored frog in the paddy soil that migrated close to the soil surface died, presumably from plowing. Aside from the 12 study frogs, several other mutilated frog corpses were found in the paddies. This species starts migrating to the soil surface during the same period when human disturbances begin, making the frogs vulnerable to these disturbances during this period. Consequently, it is necessary to facilitate the emergence of frogs to protect them from human disturbances-e.g., by temporarily filling fields with water.