Detecting developmental delays is essential for early intervention in low to middle-income countries. A cross-sectional, within-subject, comparative design was employed to determine the performance of the Parents Evaluation of Developmental status (PEDS) tools smartphone application and the Bayley Scales of Infant and Toddler Development III (BSID III) to detect developmental delays in 174 young children aged 3–18 months. Data were collected at a primary healthcare (PHC) clinic in an underserved high-risk community in South Africa. The PEDS tools identified 56% (n = 97), and the BSID-III 35% (n = 61) of the 158 children with possible developmental delays, with an overall agreement of 65% between tests. The PEDS tools referral rate was significantly higher (p = 0.004) than that of the BSID-III. The high-risk nature and age group may have contributed to poor agreement across tools. A combination of tools for screening and assessment in infants in a South African PHC context may be necessary.