OBJECTIVE: To study the effect of prenatal Zika virus (ZV) infection on brainstem function reflected in brainstem auditory evoked potentials (BAEPs). METHODS: In a cross-sectional study in 19 children (12 girls) with microcephaly related to ZV infection, aged between 12 and 62 weeks, the brainstem function was examined through BAEPs. The latencies of wave peaks I, III, and V of the left and right ears (n = 37) were standardized according to normative data, and compared between them by 2-tailed t test. The confounding variables (cephalic perimeter at the born and chronological age) were correlated with the normalized latencies using Pearson test. RESULTS: All patients showed, in general, clear waveforms, with latencies within 3 SDs of the normative values. However, statistically increased latencies of waves I and III (I > III, p = 0.031) were observed, relative to wave V (p < 0.001), the latter being closer to respective normative value. The latency of wave I was observed to increase with age (r = 0.45, p = 0.005). The waves, in turn, did not depend on cephalic perimeter. CONCLUSIONS: These results are consistent with the functional normality of the brainstem structure and its lack of correlation with microcephaly, suggesting that the disruption produced by the ZV infection does not act in the cell proliferation phase, but mostly in the processes of neuronal migration and differentiation in the telencephalon.