Background: Negative lifestyle trends are reflected in overweight and obese children, in which their lack of physical activity results in decreased muscle mass. This study aimed to define age- and sex-specific reference curves for body fat mass (BFM), skeletal muscle mass (SMM), fat-free mass (FFM), and percent body fat (%BF) in Czech children. Methods: Body composition was measured by segmental bioelectrical impedance (BIA, InBody 720). The research sample included 2093 children aged 6–11 years (1008 boys and 1085 girls). Only children whose parents provided informed consent were included. Statistical analysis was performed using SPSS v. 22. The statistical analysis was performed separately by age and sex. Anthropometric data were summarized as means and standard deviation. The percentile curves (P3, P10, P25, P50, P75, P90, and P97) of BFM, FFM, %BF, and SMM were calculated using the gamlss package in R 3.4.2 (R Foundation for Statistical Computing, Vienna, Austria). Results: This study developed age- and gender-specific percentile curves of SMM, FFM, BFM, and %BF for Czech children aged 6–11 years. During childhood, BFM and %BF increased in boys, peaking at approximately 11 years of age. Girls displayed a different pattern of age-related changes in BFM and %BF compared to that in boys. These parameters gradually increased during childhood. This pattern was also observed for SMM and FFM in both sexes. Conclusions: The purpose of this study was to serve as a reference to improve methods to evaluate body composition in Czech children and for comparison with studies worldwide.