The autonomic nervous system (ANS) acts as a central regulator of socioemotional and physiological processes. Individual differences in ANS activity are associated with mental and physical health outcomes across the lifespan, stabilizing over the first 5 years of life. Thus, ANS activity has become a focus of developmental research. Current approaches to assessing ANS are often infeasible for deployment in large epidemiological studies and low resource settings, necessitating new approaches. The goal of the current study was to compare a “gold standard” system (BioRadio) to a new system (Mawi), which offers advantages of ease of use and automated scoring pipelines, in a sample of children in Malawi, an African country with one of the lowest per capita incomes in the world. Twenty-five children, aged 3 to 6 years, were assessed simultaneously with the two systems while participating in a standardized stressor protocol that included baseline, stressor, and recovery periods. Multiple ANS indicators outputted from each system were compared. Analyses assessed agreement in equivalent indices. Absolute heart rate scores were consistently higher from Mawi; consequently, other absolute scores were consistently higher or lower, depending on the index. After adjusting for index score mean differences between systems, agreement was good to excellent (ICC 0.75-0.97). There were no differences between systems in the detection of changes in ANS activity across the baseline, stressor, and recovery episodes of the protocol. The results provide initial evidence that the Mawi system produces data sufficiently similar to that of a gold standard to be considered valid. Thus, the Mawi system may be a feasible option for measuring ANS indicators, with particular utility under certain resource constraints. Future efforts to further validate the Mawi system should include testing in a variety of settings and contexts with larger sample sizes.