This paper presents a robust adaptive iterative learning control (ILC) algorithm for 3-DOF permanent magnet (PM) spherical actuators to improve their trajectory tracking performance. The dynamic model of a PM spherical actuator is a multivariable nonlinear system with interaxis coupling terms. Uncertainties such as modeling errors, loads, and external disturbances exist in the model unavoidably, which will affect the performance, including the precision of the control system. Hence, to compensate for these uncertainties, a new hybrid control scheme that consists of a proportional–derivative (PD) feedback control with varying gains, a PD-type ILC with adjustable gains, and a robust term is developed. The new control law combines the advantages of simplicity and easy design of the PD control, the effectiveness of the ILC to handle model uncertainties and repetitive disturbances, and the robustness of the robust term to random disturbances. In addition, to expedite the convergence rate, the gains in the PD feedback control and the PD-type ILC are adaptively adjusted according to the iteration times. It is shown that the system tracking error approaches zero as the number of iterations increases. To demonstrate the proposed algorithm and verify the established theoretical results, both simulations and experiments are conducted. The results have shown that the proposed control algorithm can effectively compensate for various uncertainties and can thus improve the trajectory tracking performance of spherical actuators.