Recently, the increase in the use of fast and reliable communication systems has increased the significance and utilization of satellite-based communication systems. The communication systems used in the space environment is more reliable and robust as compared to communication systems used on earth. Because unlike ground communication, the communication systems in space have to bear harsh space environment and its effects like radiations, pressure, and vacuum, which causes anomalies in communication systems. These effects are known as Single Event Effects (SEE), which results in loss of data or sometimes even damage to the equipment. Like ground systems, in satellite, the Advanced Encryption Standard (AES) is a widely used encryption algorithm which is not only used to provide data confidentiality but also used in data authentication & integrity algorithms (e.g. CMAC) as well as in authenticated encryption (AE) algorithm (e.g., AES-GCM). The Substitution Box (S-Box) is a main component of the AES algorithm, which is generally implemented on memory blocks. The memory blocks in space are vulnerable to radiations and mostly affected by SEE; hence, protection techniques against SEE are proposed by researchers. Two methods for implementation of the S-Box algorithm are by a look-up table or by an algorithm. In this work, analysis of using these two methods of the S-Box implementation for SEE is performed. The implementation of both methods is performed on FPGA, and results show that the algorithm implementation is more reliable in the space environment as compared to table-based implementation.