A serial battery charger has a battery matrix with switches that are configured by a microcontroller that reads voltages between batteries to determine if each battery is fully-charged, charging, or absent. A switch configuration allows charging and discharging currents to flow simultaneously, and allows discharging current but blocks charging current from fully-charged batteries to prevent over-charging. The charging current flows through all charging batteries in series while the discharging current flows from all fully-charged and charging batteries in series. Blocking and bypass switches route the charging current to all charging batteries in series, but bypass all fully-charged and absent batteries. The blocking and bypass switches route the discharging current serially through all fully-charged and charging batteries in the battery matrix while avoiding absent batteries. The switches are controlled by the switch configuration from the microcontroller. Larger battery matrixes have row and column lines that are connected by connecting switches.