A backstepping-based adaptive controller with neural compensator is designed for harmonic suppression in a three-phase active power filter (APF). The fundamental rule of backstepping method is to take some state variables as “virtual controls” and then design intermediate controller. An adaptive neural controller using radial basis function (RBF) is derived to estimate the APF system nonlinearity and strengthen the current’s tracking property and power grid quality. Simulations studies indicate the proposed backstepping-based adaptive neural controller has good current tracking behavior and increased power quality.