Facial expressions provide key information for successful social interactions. Recent research finds that accurate perception of emotion expressions decreases when faces are presented with face masks. What is unknown is how individual differences in social intelligence may influence perception of masked emotion expressions. In this study, participants (n = 224) completed an emotion perception task of face stimuli presented with and without face masks and completed two measures of social intelligence: the Reading the Mind in the Eyes Test (RMET) and the Tromsø Social Intelligence Scale (TSIS). Face masks were found to significantly decrease the accurate identification of emotion expressions, impacting the perception of disgust and sad expressions the most. Further, the type of emotion misattributed to facial expressions varied across expressions. Performance on the RMET test did predict perception accuracy, while scores on the TSIS did not. As face masks continue to be common globally, we must be aware that they cause interference with our social interactions and perceptions. Further, some individuals may be more negatively impacted by these effects than others. As such, it is important that we find ways to ensure that we are effectively communicating with one another and have patience when perception mistakes arise.