Although facial muscles are heavily involved in emotional expressions, there is still a lack of evidence about the role of face primary motor cortex (face M1) in the processing of facial recognition and expression. This work investigated the effects of the passive viewing of different facial expressions on face M1 and compared data with those obtained from the hand M1. Thirty healthy subjects were randomly assigned to two groups undergoing transcranial magnetic stimulation (TMS) of face or hand M1. In both groups, short-latency intracortical inhibition (SICI) and intracortical facilitation (ICF) were probed in the depressor anguli oris (DAO) and first dorsal interosseous (FDI) muscles 300 ms after presentation of a picture of a face that expressed happy, sad or neutral emotions. Statistical analysis of SICI showed a non-significant effect of muscle (F1,28 = 1.903, p = 0.179), but a significant effect of emotion (F2,56 = 6.860, p = 0.004) and a significant interaction between muscle and emotion (F2,56 = 5.072, p = 0.015). Post hoc analysis showed that there was a significant reduction of SICI in the DAO muscle after presentation of a face with a happy expression compared with a neutral face (p < 0.001). In the FDI, a significant difference was observed between neutral and sad expressions (p = 0.010) No clear differences in ICF were detected. The different responses of face and hand muscles to emotional stimuli may be due to their functional roles in emotional expression versus protection of the body.