The last decades have seen an increasing interest in the phenomenon of yawning and the dynamics of its modulation, yet no widespread consensus exists on its origins and potential functions. Although most scholars have focused on its potential physiological functions, e.g., related to thermoregulation, arousal modulation or cortisol levels and distress, an emerging line of research has been also investigating the social implications of yawning, including its hypothesized relationship with empathy. In order to explore the dynamics of yawning modulation in infants, we investigated whether a social perturbation-like the one induced by the Face to Face Still Face paradigm, a procedure designed to assess socio-emotional regulation in infants-affects yawning and self-touch hand movements behavior in three-months old infants. As the Still Face episode represents a source of mild distress, we hypothesized that during this phase yawns would be more frequent. Moreover, through the use of path analysis, we investigated potential dynamics of facilitation, inhibition or covariance between the frequencies of these behavioral patterns. Our results showed a sharp increase in self-touch hand movements as well as in the likelihood of yawning during the stressful phase of the procedure (still-face) compared with the two minutes of face-to-face interaction and the reunion episode. Regressions also showed a higher incidence of yawns among girls, consistently with the hypothesis that the analysis of yawning behavior might capture subtle differences in regulatory strategies of infants, possibly related to the transient sex-specific activation of the hypothalamic-pituitary-gonadal axis known as mini-puberty. The path analysis showed a greater consistency between the frequencies of self-touch hand movements during the three episodes of the procedure, compared with yawning. This finding could be a result of distinct yawning-regulating mechanisms being at play in different conditions, e.g., a modulation related to stress and one to social interaction. Taken together, these results suggest that human yawning regulation is an irreducibly complex and multifaceted phenomenon since early age. Moreover, the gender differences highlighted might suggest an early diversification in yawning modulation.