Background: Cross-sectional studies detected associations between physical fitness, living area, and sports participation in children. Yet, their scientific value is limited because the identification of cause-and-effect relationships is not possible. In a longitudinal approach, we examined the effects of living area and sports club participation on physical fitness development in primary school children from classes 3 to 6. Methods: One-hundred and seventy-two children (age: 9-12 years; sex: 69 girls, 103 boys) were tested for their physical fitness (i.e., endurance [9-min run], speed [50-m sprint], lower- [triple hop] and upper-extremity muscle strength [1-kg ball push], flexibility [stand-and-reach], and coordination [star coordination run]). Living area (i.e., urban or rural) and sports club participation were assessed using parent questionnaire. Results: Over the 4 year study period, urban compared to rural children showed significantly better performance development for upper- (p = 0.009, ES = 0.16) and lower-extremity strength (p < 0.001, ES = 0.22). Further, significantly better performance development were found for endurance (p = 0.08, ES = 0.19) and lower-extremity strength (p = 0.024, ES = 0.23) for children continuously participating in sports clubs compared to their non-participating peers. Conclusions: Our findings suggest that sport club programs with appealing arrangements appear to represent a good means to promote physical fitness in children living in rural areas.