The purpose of the present study was to evaluate effect of depth of general anesthesia on the threshold of electrically evoked compound action potential in cochlear implantation. A prospective clinical study in a single-subject design was conducted in the cochlear implant center of a tertiary care University-based hospital. Sixty-one cochlear-implanted children with bilateral, severe to profound sensory neural hearing loss were enrolled in the study. During the operation electrically evoked compound action potentials (e-ECAP) were measured in two phase of general anesthesia; in deep and in light anesthesia. Thresholds of e-ECAP in these two phases of anesthesia were compared. Thirty-one children received HiRes90k1j prosthesis and 30 children received CI24RE prosthesis. Thresholds difference of electrically evoked compound action potential between light and deep anesthesia in all tested electrodes in either group were statistically significant (P < 0.001). Non-measurable e-ECAP in some electrodes at deep anesthesia was measurable in light phase of anesthesia. Depth of anesthesia can have significant influence on e-ECAP threshold and it is important to reduce the depth of anesthesia to achieve better results.