Introduction: In the last decade, childhood obesity has become a serious public health problem, and an additional increase in prevalence occurred at the beginning of the COVID-19 pandemic. In order for children to acquire life habits that they will keep in adulthood, it is necessary to follow the recommended guidelines for physical activity, a sedentary lifestyle and the sleep duration. The aim of the first research was to investigate if the body mass index (BMI) increased during the pandemic compared to the period prior, analyzing trends associated with sex, urban-rural area, and physical activity status of children in Split-Dalmatia County (SDC). The aim of the second research was to analyse the level of physical activity, sedentary lifestyle and sleep duration in order to observe the differences between children in relation to urban-rural areas and sex in SDC. Methods: The first retrospective research encompassed data derived from physical examinations of the complete population of primary school children within the SDC, conducted over a span of ten years. A total of 103,804 first, fifth and eighth grade students participated in the analysis. The second cross-sectional research included 648 parents/guardians who filled out a questionnaire for 10- and 11-year-old fifth-grade primary school students from SDC. Results: The first research findings showed that BMI values increased during the pandemic in all students, except for eighth-grade girls. In a period of 10 years, first-graders from urban areas were excessively overweight and obese, while fifth- and eighth-graders in experienced these problems in rural areas. In the first and eighth grades, girls exhibited higher rates of overweight and obesity, while boys were in the fifth grade. A decline in physical activity has been associated with an increase in BMI for both boys and girls, with a particularly pronounced effect observed in girls. During the pandemic, the situation further worsened. Second research showed that children from urban areas spend more time in physical activity and a sedentary lifestyle. Boys were more physically active, while girls were more sedentary, except for the use of electrical devices on weekends. There were no urban-rural and sex differences regarding the total sleep duration. Children from rural areas slept longer when school was in the morning. Girls slept more than boys when school was in the afternoon. Conclusions: This research can be useful to public health professionals, kinesiologists and experts from the educational system, with the aim of developing a strategy to promote awareness of healthy lifestyle habits among children and create new policies for SDC and surrounding areas that show economic and cultural parallels.