Gear manufacturers must make decisions about the manufacturing materials and superficial treatments. The best performance as to a type of failure should be evaluated. However, it is a time-demanding and costly process. The present work proposes a methodology for a comprehensive assessment (experimental and computational) of contact fatigue of gears in FZG test rig. The materials investigated were 18CrNiMo7-6 and 20MnCr5 alloy steels, widely used in industrial and automotive transmission systems, but with very different raw material costs, which can exceed twice the first compared to the second. The study evaluated the contact analysis between gears from the macroscopic point of view and the microscopic (inclusion of roughness). At the same time, the evolution of roughness and pit-damaged area after each test stage was monitored. The approach determined the stress field after each loading cycle and thus correlating the regions of higher stresses with surface and subsurface fatigue (micropitting and pitting). In addition, Weibull’s statistical analysis and SEM-EDS observations were executed. In many cases, the methodology correlated the increased roughness and pitting affected area with the regions submitted to the higher contact stress. Observations by SEM-EDS revealed that the occurrence of plastic deformation as a mechanism of wear should be considered in the equations of microscopic stress analysis. The similar fatigue life of such different materials may be correlated to the competitive mechanisms of higher mechanical strength of 18CrNiMo7-6 and better crack propagation characteristics of 20MnCr5. The methodology proved to be consistent for fatigue failure analysis of gears in FZG test rig.