Abstract Background Social-emotional difficulties in early childhood are associated with a range of outcomes across the life course and are related to socioeconomic factors. The aim of this study was to examine intersectional inequalities in social-emotional problems in preschool children relating to their parents’ income, education and country of birth in addition to investigating the public health implications. Methods This population-based study with a repeated cross-sectional design in the Västerbotten County of Sweden used the Ages and Stages Questionnaires: Social-Emotional (ASQ:SE) for children aged 3 in child health care services over the years of 2014-2018 and socio-economic information from national population registers. The effective sample of 8,823 individuals was analyzed using additive binomial regression in combination with an analysis of individual heterogeneity and discriminatory accuracy (AIHDA) approach to estimate risk differences for social-emotional problems across 27 intersectional groups and discriminatory accuracy. Results Average risk differences generally increased in the groups where multiple dimensions of social inequality intersected, with risk differences as high as 18% (95% CI 8 to 28%) and 25% (95% CI 14 to 37%) compared to the most advantaged category. The discriminatory accuracy of all three included regression models was estimated as moderate, but improved in a slight but statistically significant way with the addition of social inequalities. Conclusions This study increases our understanding of intersectional and social inequalities in social-emotional problems in preschool children. It supports the need for universal public health policies in addition to policies targeting more vulnerable groups when addressing this issue, consistent with the concept of proportionate universalism. An intersectional research perspective including discriminatory accuracy could increase our knowledge of health inequities and improve public health effectiveness. Key messages • Intersecting dimensions of social inequalities are associated with an increased risk of social-emotional problems in children aged 3. • Universal public health policies are needed in addition to policies targeting vulnerable population groups with regards to social-emotional problems in young children.