Facial expressions are complex and subtle signals, central for communication and emotion in social mammals. Traditionally, facial expressions have been classified as a whole, disregarding small but relevant differences in displays. Even with the same morphological configuration different information can be conveyed depending on the species. Due to a hardwired processing of faces in the human brain, humans are quick to attribute emotion, but have difficulty in registering facial movement units. The well-known human FACS (Facial Action Coding System) is the gold standard for objectively measuring facial expressions, and can be adapted through anatomical investigation and functional homologies for cross-species systematic comparisons. Here we aimed at developing a FACS for Japanese macaques, following established FACS methodology: first, we considered the species’ muscular facial plan; second, we ascertained functional homologies with other primate species; and finally, we categorised each independent facial movement into Action Units (AUs). Due to similarities in the rhesus and Japanese macaques’ facial musculature, the MaqFACS (previously developed for rhesus macaques) was used as a basis to extend the FACS tool to Japanese macaques, while highlighting the morphological and appearance changes differences between the two species. We documented 19 AUs, 15 Action Descriptors (ADs) and 3 Ear Action Units (EAUs) in Japanese macaques, with all movements of MaqFACS found in Japanese macaques. New movements were also observed, indicating a slightly larger repertoire than in rhesus or Barbary macaques. Our work reported here of the MaqFACS extension for Japanese macaques, when used together with the MaqFACS, comprises a valuable objective tool for the systematic and standardised analysis of facial expressions in Japanese macaques. The MaqFACS extension for Japanese macaques will now allow the investigation of the evolution of communication and emotion in primates, as well as contribute to improving the welfare of individuals, particularly in captivity and laboratory settings.