Purpose: to investigate the frequency-following response (FFR) for sustained neural activity. Methods: 39 individuals, aged between 20 to 47 months old were divided into 2 groups: (i) 20 individuals without prenatal exposure to the congenital Zika syndrome (CZS) or hydrocephaly, normal development, no risk factors for hearing loss or syndromic hearing impairment and (ii) 19 individuals diagnosed with CZS and microcephaly -based on imaging studies linked to the clinical presentation of the condition. All participants exhibited normal click-ABR tests. FFR waveforms were documented using the /da/ syllable employing the Navigator Pro. The statistical analysis used was ANOVA (p-value <0.05). Results: no distinctions were observed concerning the variables of group, age, or gender with respect to FFR latency values, except for an interaction between gender and group for latency values associated with waves V and F. Children with CZS and microcephaly showed a difference for latency values in wave V for both males and females, when compared to the control group. Conclusion: children presented with CZS and microcephaly showed higher average latencies for waves V, A, C, D and F (male) compared to the control group, whereas, in waves E, F (female) and O they showed higher values in the control group.