The Experimental Power Reactor (EPR) design was developed in Indonesia based on HTGR technology and employed fully-digitized system for reactor instrumentation and control. The field programmable gate array (FPGA) technology which has advantages in minimizing a common cause failure and vulnerability from the cyber- attack was employed in the design of control rod drive system (CRDS) of EPR. This paper discusses the process in developing of FPGA-based CRDS for EPR using the V-Model approach. Verification and adjustment were conducted toward the CRDS design requirement established in the preliminary research based on relevant design criteria, standard, and most recent data. The rule checking method has been used to verify that specified rules and criterias have been adhered. In this study a simulation prototype was designed and implemented into Digilent Basys3 FPGA board in order to conduct a thorough design verification and validation process. The results showed the conformity of system requirements with the corresponding standard and design criteria. In addition, the use of simulation prototypes will be beneficial for verification process and tends to increase the effectiveness of V-model in the development of control system for CRDS. The approach used in this study can be applied to designing other FPGA-based systems of EPR.