The School Entry Examination (SEE) can be used to identify children with current health issues, developmental delays, and risk factors for later diseases. This study analyzes the health status of preschool children in a German city with considerable socio-economic differences among its quarters. We used secondary data from SEEs 2016–2019 from the entire city (8417 children), which we divided into quarters with low (LSEB), medium (MSEB), and high socioeconomic burden (HSEB). In HSEB quarters, 11.3% of children were overweight as opposed to 5.3% in LSEB quarters. In HSEB quarters, 17.2% of children had sub-par cognitive development in contrast to 1.5% in LSEB quarters. For overall sub-par development, LSEB quarters had a prevalence of 3.3%, whereas, in HSEB quarters, 35.8% of children received this result. Logistic regression was used to determine the influence of the city quarter on the outcome of overall sub-par development. Here, considerable disparities among HSEB and LSEB quarters remained after adjustment for parents’ employment status and education. Pre-school children in HSEB quarters showed a higher risk for later disease than children in LSEB quarters. The city quarter had an association with child health and development that should be considered in the formulation of interventions.