Background: The prevalence of obesity and overweight in children is increasing in industrialized countries. Monitoring the evolution of these phenomena is essential for understanding prevention and health promotion programs. This study aims to present the analysis of anthropometric data collected by school nurses from the School Health Service of Geneva (Service de santé de l'enfance et de la jeunesse) for children aged 5 to 6 years during the 2021-2022 school year, as well as describe the trends in overweight and obesity from 2003-2004 to 2021-2022. Risk factors were also assessed in the 2021-2022 sample. Methods: This study included a random sample of 958 (479 girls and 479 boys) primary school pupils aged 5 to 6 years in Geneva. Data on weight, height and socioeconomic status were collected. BMI was analyzed using the Cole standard. A multivariate analysis was conducted to assess the influence of socioeconomic factors on overweight and obesity. We compared these results with BMI trends in students of the same age since 2003. Results: In 2021-2022, overall prevalence of overweight was 12.73%, and obesity was 5.64%. Girls had higher rates of overweight (14.20%) and obesity (6.68%) compared to boys (11.27% and 4.59%, respectively) (p < 0.0001). Overweight in boys significantly increased since the 2013-2014 and 2019-2020 measurements (p = 0.003). The trend for girls was similar but not statistically significant. Obesity rates have not significantly increased since 2019-2020 in both genders, but there is a significantly increasing trend for girls since 2013-2014 p = 0.045). Socioeconomic factors, particularly the socioeconomic class of parents, played a predictive role in overweight and obesity. Conclusions: The School Health Service of Geneva and the Directorate General of Health have a crucial role in monitoring and preventing childhood obesity. The prevalence of overweight and obesity has remained high since 2010, justifying continuous efforts for prevention. A significant increase in prevalence has been observed since 2020, particularly among overweight boys, and could be related to COVID-19 confinement measures.