System and methods for balancing a vehicle battery system are presented. In certain embodiments, a method for balancing battery system having multiple battery sections may include receiving estimated states of charge of the battery sections. Based on the estimated states of charge, a determination may be made whether the battery sections have states of charge within one of plurality of regions included in a state of charge window. Based on the determination, one of a plurality of different balancing algorithms may be utilized to control transfer energy between the battery sections to balance the battery sections.