Objective:The main aim of this study was to determine the impact of botulinum toxin A (BTX-A) on severity and frequency of drooling in children with Cerebral Palsy (CP) secondary to Congenital Zika Syndrome (CZS). Methods: This is a prospective longitudinal observational study including 23 children who received bilateral injections of BTX in the parotid and submandibular glands. The Thomas-Stonell & Greenberg Drooling Severity and Frequency Scale was applied by a multidisciplinary team including Speech, Language and Hearing professionals. The Global Impression of Improvement (GII) Scale was also applied to assess parents' subjective perceptions of therapeutic response. Swallowing was assessed using Doppler ultrasonography. Univariate logistic regression was used to analyse differences between responders and non-responders. Results: Participant age varied from 27 to 38 months (mean 31.78, SD = 2.61) all presented with Gross Motor Function Classification System (GMFCS) V. Drooling Severity and Frequency Scale scores ranged from 7 to 9 points (median = 9) prior to BTX administration and from 4 to 6 (median = 6) after. Pre-and post-treatment reduction in drooling severity occurred (Z = −3.746; p < 0.001). No cases of drooling worsening were reported. Only two subjects presented adverse effects attributed to BTX administration. Correlation was only confirmed with GII. Discussion: This article presents the safe and positive impact of BTX-A administration guided by anatomical references described in the literature, even on children with microcephaly. Further studies are needed to facilitate the use of Doppler ultrasonography as a tool to characterize changes in sensory processing and motor response following intraoral input in children with CP.