A medical apparatus system includes a first communication section provided in a medical apparatus and configured to transmit battery use information including information concerning a residual capacity of a first battery, a charger including a power supply section configured to charge a second battery, and a control section configured to set a charging current of the power supply section on the basis of the battery use information and battery charging information including a residual capacity of the second battery such that a capacity insufficiency residual time, which is time until the residual capacity of the first battery changes to a state of residual capacity insufficiency, is equal to or longer than a charging completion residual time, which is time until the second battery changes to a completely charged state.