Side-channel attacks pose a severe threat to both software and hardware cryptographic implementations. Current literature presents various countermeasures against these kinds of attacks, based on approaches such as hiding or masking, implemented either in software, or on register–transfer level or gate level in hardware. However, emerging trends in hardware design lean towards a system-level approach, allowing for faster, less error-prone, design process, an efficient hardware/software co-design, or sophisticated validation, verification, and (co)simulation strategies. In this paper, we propose a Boolean masking scheme suitable for high-level synthesis of substitution–permutation network-based encryption. We implement both unprotected and protected PRESENT, AES/Rijndael and Serpent encryption in C language, utilizing the concept of dynamic logic reconfiguration, synthesize it for Xilinx FPGA, and we compare our results regarding time and area utilization. We evaluate the effectiveness of proposed countermeasures using both specific and non-specific t-test leakage assessment methodology. We discuss the leakage assessment results, and we identify and discuss the related limitations of the system-level approach and the high-level synthesis.