Abstract Introduction The infection caused by Zika virus during pregnancy leads to congenital Zika syndrome (CZS). In a previous study of our group, we found that the heart is smaller in children with CZS, with few functional alterations. Left atrial strain imaging enables quantitative assessment of left atrial function, and recently its application has also shown promise in the pediatric population. Purpose To evaluate left atrial function in children affected by CZS, using echocardiogram and speckle tracking imaging technique. Methods This observational study was conducted with children with CZS using a two-dimensional speckle tracking technique to measure left atrial reservoir strain (LAS-r), conduit strain (LAS-cd), and contraction strain (LAS-ct). Also, to investigate the relationship between LAS-r and systolic excursion of the septum and lateral mitral annular plane (MAPSE), left atrial volume index and E/e’ ratio. Results A total of 52 patients were included, the median age of the studied population was 5 years (3 to 6), 59.6% male, and the body surface area was 0.66 [0.51, 0.90]. In the echocardiographic evaluation the left atrium volume index (ml/m²) was 13.15 [6.80, 18.00], considered smaller by the reference value. Also, the LAS-r (%) was 40.99 [24-70.5], LAS-cd (%) was 30,94 [32.5-52.5], LAS-cd (%) was 10,91 [5.2-24], values considered normal by the literature. Lateral MAPSE (cm) was 1.25 [0.81, 1.86] and septal MAPSE (cm) was 0.98 [0.78, 1.66] and E/e' ratio was 7.52 [4.57, 10.78]. A positive linear correlation was found between LAS-r and lateral MAPSE (r = 0.51, P = 0.019). Conclusion This original study with children with CZS shows that despite reduced atrial volume, the left atrial function remains normal, and correlates with left ventricular function evaluated by MAPSE. Further studies are needed to prospectively analyze the follow-up of left atrial morphology and function in this population.