This paper presents the nonlinear identification and the robust position tracking control of a camless engine valve actuator in frequency domain. If a periodic signal excites a nonlinear system, it turns out to generate output spectrum at multiple harmonic frequencies other than that of the excitation. Therefore, such nonlinear features should be taken account in tracking control system design to improve tracking performance. First, nonlinear identification with a Volterra series representation is proposed to capture nonlinearities. Then, robust tracking control of an uncertain Volterra system based on the internal model principle is addressed. It argues that an internal model unit should embed the extended generating dynamics to suppress tracking error occurring at multiple harmonics. To validate the control design method, the tracking results of two different generating dynamics are compared. From the comparison, tracking performance advances through the extended generating dynamics.