Fully flexible valve actuation (FFVA) system, often referred to as camless valvetrain, employs electronically controlled actuators in place of the camshaft to drive the intake and/or exhaust valves for internal combustion engines. This system enables the engine controller to tailor the valve event according to the engine operating condition in real-time to improve fuel economy, emissions, and torque output performance. This paper presents the transient control of a laboratory electro-hydraulic fully flexible valve actuation system. Transient control of the FFVA system includes lift transient, duration transient, phase transient, speed transient, and mode transient. With constant engine speed, the valve profile is periodic in time domain and the lift, phase, and duration transients can be realized using robust repetitive control. When the engine speed varies, the period of the valve profile changes in real-time. This phenomenon poses a fundamental challenge to the transient control problem and repetitive control cannot be applied anymore. To overcome this challenge, we propose a new valve profile consisting of a periodic portion and a dwell portion with time-varying duration. Robust repetitive control is then applied to the periodic portion and proportional plus integral and derivative (PID) control is applied to the dwell portion. These two controls are switched in real-time to achieve asymptotic valve profile tracking performance. To demonstrate the effectiveness of the proposed control method, we show real-time valve-lift profiles used to explore homogeneous charge compression ignition (HCCI) combustion at different engine operating conditions.