In regions experiencing ongoing aseismic deformation, fault’s Activity Rate (AR) calculations often lead to an overestimation of hazard potential. This study proposes a novel methodology that integrates the Seismic Coupling Coefficient (SCC) into the fault Seismic Activity Rate (SAR) calculation process to discriminate seismic moment rates. We introduce FaultQuake, an open-source Python tool equipped with a Graphical User Interface (GUI), designed to implement this methodology and accurately estimate SAR for faults. These activity rates can be included in Probabilistic Seismic Hazard Assessment (PSHA) frameworks and assist in differentiating the seismic and aseismic deformation. FaultQuake also presents an innovative embedded workflow, the Optimal Value Computation Workflow (OVCW), based on Conflation of Probabilities (CoP), for calculating the Maximum Magnitude (Mmax) from the empirical relationships and the observed magnitudes (Mobs) assigned to a single fault. This enhancement improves the estimation of seismic moment rates and the SAR calculation process. FaultQuake outputs are provided in the format of OpenQuake engine input files to facilitate the PSHA process. We present a sample case study focusing on the PSHA of a region in southern Iran characterized by a substantial aseismic deformation to illustrate the practical application of FaultQuake in seismic hazard analysis. Peak Ground Acceleration (PGA) maps for 10% and 2% Probabilities of Exceedance (PoE) are plotted to compare PGAs with and without applying the FaultQuake algorithm. The results provide an enhanced view of the area’s hazard with mitigation of the overestimation, resulting in more representative hazard maps. The source codes of FaultQuake are available at the FaultQuake GitHub repository, contributing to the computer and geoscience community.