A battery capacity estimation system executes a charging and discharging process (S1), an alternating current impedance acquiring process (S2 and S3), and a battery capacity estimating process (S4 to S6). The charging and discharging process involves charging and discharging a target secondary battery. The alternating current impedance acquiring process involves acquiring a measurement result of an alternating current impedance of a target secondary battery, by applying an alternating current signal within a specific frequency range to the target secondary battery after completion of the charging and discharging in the charging and discharging process and before a predetermined maximum waiting time elapses. The battery capacity estimating step involves estimating a battery capacity of the target secondary battery based on the measurement result of the alternating current impedance.