The aims of this study were to identify fungal growth inhibitory substances in cheese prepared using crude enzymes from Hericium erinaceum MAFF 435060 exhibiting milk-clotting activity and elucidate the conditions under which these substances are produced. Fungal growth inhibition caused by fatty acids, such as butanoic, hexanoic, octanoic, decanoic, and 9-decenoic acids, released by lipase activity of crude enzymes during ripening was estimated. Notably, the amounts of butanoic, hexanoic, and octanoic acids in ripened cheese exceeded their minimum growth inhibitory concentrations for Aspergillus niger NBRC 105649. Growth inhibition and high fatty acid content were observed in cheese prepared using homogenized milk as raw material, although homogenized milk in which milk fat was not encapsulated within the globule membrane was required. These results suggested that the use of crude enzymes from H. erinaceum MAFF 435060 may allow the production of cheese with a prolonged shelf life.