Mother–child interaction has been characterized by a fine-tuning of behavior and physiological activity. Yet, little is known about the dynamics of mother–child physiological synchrony during early school age and their associations to positive affect. To investigate these processes, 42 mother–child dyads, with children aged 8 to 10 years, played an interactive game while their interbeat intervals (IBI) and respiratory sinus arrhythmia (RSA) were measured simultaneously. IBI/RSA synchrony was calculated using cross-correlations of the IBI/RSA second-by-second time series for lags − 3 to + 3 seconds. Mother’s and child’s individual and shared positive affect were microcoded. During the interactive tasks, IBI and RSA synchrony significantly increased compared to control conditions. RSA and affect synchrony were significantly stronger for negative compared to positive lags indicating a stronger child leads/mother follows covariation. Further, dyad’s IBI and RSA synchrony were significantly associated to mother’s and child’s individual positive affect. Our data suggest that in low-risk community samples, mothers may respond to their children’s positive affect by matching their own affect and physiology. Investigating these temporally precise, concurrent and lagged synchrony processes may open up new avenues for understanding the ways in which parent–child interactions contribute to child developmental outcomes.