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We surveyed pediatric primary care clinicians working in Federally Qualified Health Centers about their perceptions of children’s social-emotional wellbeing. We identified clinician’s current methods for assessing social-emotional wellbeing in practices, perceived implementation barriers to providing behavioral health care, and interest in adopting a validated, low-burden developmentally sensitive parent-report instrument for screening for social-emotional wellbeing in young children. We surveyed 72 PCCs working in FQHCs from 9 US states. Analyses included examining central tendencies, correlations, analysis of variance, and group differences via t-tests. Average PCC perceptions of social-emotional wellbeing importance for overall health were statistically significantly higher than their confidence in providing care for common social-emotional wellbeing concerns (mean difference = 1.31, 95% CI = 1.13–1.49). PCCs expressed low satisfaction with currently available screening measures for identifying concerns in social-emotional wellbeing. Fewer than half of clinicians reported using any standardized parent-reported measure for identifying concerns in social-emotional wellbeing. Assessment methods and decision tools that improve clinician confidence concerning risk indications are needed, particularly at the critical early childhood period. Policymakers and payers ought to facilitate funding mechanisms that support pediatric PCCs in identifying early concerns in social-emotional wellbeing and providing referral guidance to evidence-based interventions to support parents and caregivers.