A battery controller of an embodiment includes an auxiliary battery, a connection control unit, a calculating unit, and a balancing control unit. The auxiliary battery is a lithium ion secondary battery that is connectable to or disconnectable from an auxiliary power line of a vehicle. The connection control unit disconnects the battery from the auxiliary power line under a certain condition of the vehicle. The calculating unit calculates the state of charge of the battery when the battery is disconnected by the connection control unit. The balancing control unit executes balancing control to equalize the amount of charge between cells of the battery when the battery is disconnected by the connection control unit.