Custom reverse shoulder implants represent a valuable solution for patients with large bone defects. Since each implant has unique patient-specific features, finite element (FE) analysis has the potential to guide the design process by virtually comparing the stability of multiple configurations without the need of a mechanical test. The aim of this study was to develop an automated virtual bench test to evaluate the initial stability of custom shoulder implants during the design phase, by simulating a fixation experiment as defined by ASTM F2028-14. Three-dimensional (3D) FE models were generated to simulate the stability test and the predictions were compared to experimental measurements. Good agreement was found between the baseplate displacement measured experimentally and determined from the FE analysis (Spearman's rank test, p < 0.05, correlation coefficient ρs = 0.81). Interface micromotion analysis predicted good initial fixation (micromotion <150 μm, commonly used as bone ingrowth threshold). In conclusion, the finite element model presented in this study was able to replicate the mechanical condition of a standard test for a custom shoulder implants.