The simultaneous recording of brain activity in two or more people, termed hyperscanning, is an emerging field of research investigating the neural basis of social interaction. Hyperscanning studies of adult–infant dyads have great potential to provide insights into how social functions develop. In particular, taking advantage of functional near-infrared spectroscopy for its spatial resolution and invulnerability to motion artifacts, adult–infant fNIRS may play a major role in this field. However, there remains a problem in analyzing hyperscanning data between adult and (...) young populations. Namely, there are intrinsic differences in hemodynamic time latencies depending on age, and the peak latency of the hemodynamic response function is longer in younger populations. Despite this fact, the effects of such differences on quantified synchrony have not yet been examined. Consequently, the present study investigated the influence of intrinsic hemodynamic differences on wavelet coherence for assessing brain synchrony, and further examined the statistical removal of these effects through simulation experiments. First, we assumed a social signal model, where one counterpart of the dyad sends a social signal to the other, which eventually results in simultaneous brain activation. Based on this model, simulated fNIRS activation sequences were synthesized by convolving boxcar event sequences with HRFs. We set two conditions for the event: synchronized and asynchronized event conditions. We also modeled the HRFs of adults and infants by referring to previous studies. After preprocessing with additional statistical processing, we calculated the wavelet coherence for each synthesized fNIRS activation sequence pair. The simulation results showed that the wavelet coherence in the synchronized event condition was attenuated for the combination of different HRFs. We also confirmed that prewhitening via an autoregressive filter could recover the attenuation of wavelet coherence in the 0.03–0.1 Hz frequency band, which was regarded as being associated with synchronous neural activity. Our results showed that variability in hemodynamics affected the analysis of inter-brain synchrony, and that the application of prewhitening is critical for such evaluations between adult and young populations. (shrink)