Purpose: The aim of this research was to describe, examine, and compare the level of physical fitness, physical activity, and sedentary behaviour in pupils aged 6–13 in the Region of Murcia, Spain, in accordance with weight status. Methods: A total of 370 children (166 girls and 204 boys) aged 6–13 (M = 8.7; DT = 1.8) from the Region of Murcia participated in this descriptive and cross-sectional study. Some anthropometric parameters such as body mass index, waist circumference, as well as skinfold measurements were determined. ALPHA-FIT Test Battery was used to evaluate physical fitness. Krece Plus Short Test was used to measure physical activity level and sedentary behaviour. Results: 52.4% of the children presented excess weight (according to the World Health Organization growth references). Regarding boys, statistically significant differences were found for cardiorespiratory fitness (p < 0.001), relative handgrip strength (p < 0.001), lower muscular strength (p < 0.001), speed-agility (p < 0.001), as well as sport activities hours (p = 0.001) among the three weight status groups (normal weight, overweight, and obesity). As for girls, statistically significant differences were found for cardiorespiratory fitness (p = 0.004), relative handgrip strength (p < 0.001), lower muscular strength (p < 0.001), sport activities hours (p = 0.005), as well as physical activity level (assessed by Krece Plus Test) (p = 0.017). A negative statistically significant correlation was found between body mass index and cardiorespiratory fitness (rho = −0.389), lower muscular strength, (rho = −0.340), and relative handgrip strength (rho = −0.547). At the same time, a positive statistically significant relationship between body mass index and the time spent in speed-agility (rho = 0.263) was shown. Regarding waist circumference and body fat percentage, similar relationships were identified. Moreover, a greater probability of having higher cardiorespiratory fitness (OR = 1.58; CI95% = 1.38–1.82), relative handgrip strength (OR = 1.25; CI95% = 1.19–1.31), more hours of sport activities (OR = 1.40; CI95% = 1.19–1.66), and physical activity level (assessed by Krece Plus Test) (OR = 1.23; CI95% = 1.07–1.42) was noted in the normal weight group. Conclusions: Children that presented normal weight achieved higher results for health-related physical fitness and physical activity than those with excess weight; this was, however, not found to be the case for sedentary behaviour. The authors emphasise the need for changes in public policies and school-based intervention programmes to develop higher levels of both PF and PA in overweight and obese children.