In this paper, design and implementation of a digitally controlled flyback inverter with combined microcontroller and Field Programmable Gate Array (FPGA) logic is presented. A System-on-Chip (SoC) device is used to implement a digital controller for the flyback inverter consisting of a FPGA logic, a 32 bit microcontroller, and a programmable analog interface. Integrating all the necessary interfaces and digital resources into one single platform, reduces the controller power consumption, cost, and board size. This platform also brings the flexibility of partitioning the control task, and tracking each partition either on FPGA logic or on microcontroller software, thus enabling the utilization of both domains efficiently. The focus of this paper is on the use of a combination of FPGA and microcontroller through a SoC device, for the digital control of a flyback inverter with center-tapped primary winding. A prototype system, which is superior to previous approaches in view of more compact digital design, more accurate timing of pulse width modulation signals and shorter development time has been designed, implemented, and satisfactorily tested through laboratory experiments.