In this study, COx-free hydrogen production via decomposition of ammonia was investigated in the microwave reactor using carbon supported cobalt-containing catalysts. Two different carbon sources, namely mesoporous carbon and activated carbon, were utilized and catalysts were successfully synthesized following an impregnation procedure. Different characterization techniques, such as ICP-OES, X-Ray Diffraction (XRD), Nitrogen Physisorption, Transmission Electron Microscopy (TEM), Raman Spectroscopy were applied to determine the structural properties of the catalysts. Total conversion of ammonia was achieved over carbon supported cobalt catalysts at about 350–400 °C under pure ammonia flow (GHSVNH3 of 36,000 ml/gcat.h). Significantly higher conversion values could be achieved in microwave reactor due to the its superior properties, such as selective heating, compared to conventional reactor. Microwave energy would probably facilitate the recombinative desorption of bonded N atoms from cobalt active species during ammonia decomposition reaction resulted in higher conversion values comparatively lower reaction temperature.