Abstract Background Studies show that children and adolescents in the most socially deprived areas (SDA) consult their general practitioner (GP) more often than those in the least socially deprived areas (Non-SDA). Given that GPs see a wide range of diseases, it is important to know which clinical diagnoses are shaped by socioeconomic factors. The primary objective was to determine the association between area level social deprivation and consultation rates in a pediatric population. The secondary objective was to explore this association across a wide range of clinical diagnoses. Methods A cohort study using the Rijnmond Primary Care Database (RPCD) was conducted. Between 2013 and 2020, a total of 69,861 patients aged 0 to 17 years registered with a GP were analysed. A consultation was defined as patient contact and entry of a diagnosis using the International Classification of Primary Care (ICPC-1) code. Associations between consultation rates, ICPC-1 codes and area level social deprivation were explored using a Poisson regression model. The incidence risk ratio (IRR) and 95% confidence interval (CI) were reported. Results Over the 7-year study period the consultation rate of the study population was 3.8 per person-years. The top 5 reasons for children and adolescents to consult their GP was related to skin, respiratory, general unspecified, musculoskeletal and digestive symptoms or diagnoses. Consultation rate was higher in SDA group compared to Non-SDA group (IRR 1.20, 95% CI 1.19–1.20). Consultation rate for ICPC-1 code related to pregnancy and family planning was significantly lower in SDA group compared to Non-SDA group. Upon further exploration of this code, SDA group were less likely to consult for oral contraception and more likely to contact a GP for induced termination of pregnancy compared to Non-SDA group (IRR 0.36; 95% CI 0.33–0.44 and IRR 2.94; 95% CI 1.58–5.46 respectively). Conclusions Overall, SDA group had higher GP consultation rates for the majority of clinical diagnoses except for pregnancy and family planning. In this latter category, adolescent females in SDA consulted less frequently for oral contraception. This study illustrates the need to understand the underlying health seeking behaviors of children and adolescents at different development phases of their lives.