Planarians show negative phototaxis and have extensive regenerative ability, including the ability to regenerate the brain. Recently the process of regeneration of the planarian brain has been divided into three steps based on the expression of neural markers. In this study, we have analyzed the process of recovery of the light response during head regeneration. Although morphological observations indicated that regeneration of the eyes and optic nerves appeared to be completed by the fourth day, the recovery of the evasion behavior against light was not recovered within 4 days after amputation. Functional recovery of the evasion behavior could be detected starting 5 days after amputation and then gradually recovered. We previously identified genes which are specifically expressed in the brain after the recovery of morphological structures. This characteristic suggested that these genes may be involved in functional recovery of the brain. To investigate the function of these genes, we performed gene knockout analysis using the RNA interference method. The results clearly indicated that these genes are involved in the functional recovery of the visual system.