Background: In this study, we examined the development of children's moderate to vigorous physical activity (MVPA) and physical education (PE) enjoyment through the Physical Activity as Civil Skill Program 2012-2014. Methods: Participants were 661 (265 intervention, 396 control) elementary school children in central and northeast Finland. The program was implemented across 2 years with 3 measurement phases using self-reported MVPA and PE enjoyment, and accelerometer-determined MVPA of a random subsample (N = 76). Results: The proportion of children meeting the current MVPA guidelines declined from 38% to 22% (intervention) and 14% to 9% (control), whereas PE enjoyment was stable in both groups. Boys were more physically active than girls only within control group children. Teachers' feedback indicated that violence and bullying among intervention students reduced during the program, which can be considered as an additional benefit. Conclusions: It may be that both MVPA and PE enjoyment may require more tailored actions to be increased across a long-term program. It is important to ensure that school-based physical activity programs, especially including transition from elementary to middle school level, provide all children positive experiences, and thus, may improve their motivation, and MVPA participation during school days and leisure time.