This paper addresses the security of embedded systems, focusing on field-programmable gate arrays (FPGAs) and their vulnerability to side-channel attacks, particularly timing attacks. We analyze the risks associated with traditional encryption devices and propose a novel methodology to mitigate Timing Side Channel Attacks (TSSA) at the application layer. Our approach ensures constant time execution for varying input sizes, achieved through a unique sub-algorithm that adapts to input variations and maintains uniform processing times. This methodology is supplemented by a novel ‘divider’ component and random time delays to obscure execution time correlations with input data. Additionally, we introduce a technique for balancing execution costs in cryptographic systems by constructing an enhanced Abstract Syntax Tree (AST) and normalizing the weights of execution paths. This comprehensive strategy effectively secures FPGAs against timing attacks, significantly contributing to embedded system security and paving the way for future advancements in cryptographic system defense.