Background: Childhood obesity remains a significant public health challenge globally. Croatia ranks among the leading European countries in terms of childhood overweight and obesity prevalence. Methods: The present cross-sectional study analysed overweight and obesity prevalence trends from 2003 to 2022 on a nationally representative sample containing data from five studies, two independent studies and three WHO COSI rounds. Data from a total of 11,817 children aged 7.00–8.99 were analysed. Weight categories were defined using the IOTF and WHO cut-offs. Overweight and obesity prevalence rates and trends overall and by sex and region were calculated, and binary regression models applied to investigate the relationship between the risk of overweight and several variables. p-value < 0.05 was used to define statistical significance. Results: Temporal trends and associations were investigated using the IOTF reference values. The prevalence of overweight (including obesity) had increased steadily from 2003 to 2015, thereafter continuing to increase at a slower rate, whereas the prevalence of severe obesity reduced over time. Even though boys had slightly higher prevalence rates of overweight, the growth in overweight prevalence in girls over time was significant. At the regional level, the lowest prevalence rates were detected in the capital (City of Zagreb region). The risk of overweight was at least 50% higher in all the other regions in Croatia, and a rising trend in overweight risk with time was particularly high among children in the Adriatic and Northern regions. Conclusions: Despite a deceleration in the rate of increase in overweight (including obesity) prevalence, Croatia is yet to reach a plateau observed in some other European countries. Unearthed regional differences warrant further investigation.