This study presents a new flatness-based control scheme for the quantum series-parallel LCC-type resonant converter with output voltage doubler for high-voltage pulse applications, like medical X-ray imaging. Based on a previously derived continuous time model of the system, a flat output of the system model is shown. Moreover, an optimised trajectory planning algorithm with limited resonant current and the controller design are addressed. Details on the experimental set-up and the real-time controller implementation on an FPGA are given. Measurement results show the accuracy of the presented control method.