This research focuses on the tracking control design for a camless engine valve actuator during engine speed transients. The cyclic but aperiodic valve reference signal to be tracked can be modeled using two different methods, i.e., as a combination of frequency varying sinusoids in the time domain or as a repetitive (periodic) signal in the rotational angle domain. The recently developed time-varying internal model based controller is ideally suited for both the approaches. Investigation of the continuous time and discrete domain implementations uncovers some unique characteristics resulting from the time-varying nature of the system which favor working in the discrete domain. A quantitative analysis comparing various performance metrics for the different approaches of modeling the reference signal helps highlight the relative advantages of each method. Finally, experimental results from a prototype camless engine valve actuation system help validate the overall effectiveness of the proposed approach.