Subtilisin-like proteases are widely distributed and reported to be required for virulence in pathogenic fungi. In chestnut blight fungus Cryphonectria parasitica, prb1, encoding a putative subtilisin-like protease, was expressed and recombinant Prb1 protein was shown to have a protease activity in vitro. prb1-deleted mutants exhibited reduced total protease activity by 60%. The Δprb1 mutants showed a phenotype of reduced aerial hyphae, lower level of sporulation, and a significant reduction in virulence. Additionally, site-directed mutagenesis of Prb1 protein revealed that D195, H227, and S393 are critical for C. parasitica Prb1 function in vivo. Transcriptional analysis showed that deletion of prb1 also reduced the transcript accumulation levels for genes encoding key components of the heterotrimeric G-protein signaling pathway, including cpga1, cpgb1, cpgc1, and ste12. Furthermore, deletion of prb1 results in the accumulation of autophagic bodies in the fungus. Taken together, our results showed that prb1-encoded protease functions in the regulation of virulence, phenotypical traits, and autophagy in C. parasitica.