Camless valve actuation systems, also referred to as Fully Flexible Valve Actuation systems, use electronically controlled actuators to replace the camshaft in an internal combustion engine. This paper presents the control design for such an actuation system to enable the precise valve motion control during engine speed transients. The desired valve motion (reference) remains periodic in the crank angle domain, but becomes cyclic and aperiodic in the time domain when the engine speed changes in real-time. This phenomenon motivates the control design in the rotational angle domain. However, this approach results in a time-varying model for the plant. A systematic method for obtaining the discrete time-varying Input/Output representation of higher order systems is developed to enable the application of the newly developed time-varying repetitive control to plants with complex dynamics. The use of a variable sampling rate helps accurately represent complex reference signals using low dimensional models. The implementation of the simulations on a rapid control prototyping system helps identify and address potential issues that influence the controller execution time which directly affects the maximum engine speed at which it can be used.