Schools are key settings for the promotion of students' physical activity, fitness, and motor competence. The purpose of our study was to investigate the efficacy of a 5-month-long intervention program that aimed to increase students' motor competence and health-related fitness during school days. We conducted a quasi-experimental study with 325 Finnish Grade 5 (Mage = 11.26, SD = 0.33) students from five schools. Two schools were allocated to the intervention group and three schools to the control group. The intervention consisted of three components: (a) weekly 20 min session during regular PE lessons, (b) weekly 20 min session during recess, and (c) daily 5-minute-long classroom activity breaks. All activities were designed to systematically develop different elements of motor competence and fitness. The following assessments were conducted at baseline and 5-months: cardiorespiratory fitness levels were measured by 20-meter shuttle run test, muscular fitness by curl-up and push-up tests, and motor competence by 5-leaps and throwing-catching combination tests. We analyzed the data using a multi-group latent change score modeling. Results showed that students in the intervention group developed significantly better in 20-meter shuttle run test (β = 0.269, p = 0.000, 95% CI [0.141, 0.397]; +5.0 laps), push-up (β = 0.442, p = 0.000, 95% CI [0.267, 0.617]; +6.5 repetitions), curl-up (β = 0.353, p = 0.001, 95% CI [0.154, 0.552]; +7.8 repetitions), and throwing-catching combination tests (β = 0.195, p = 0.019, 95% CI [0.033, 0.356]; +1.1 repetitions) than students in the control group. The intervention program appeared to be feasible and effective in increasing students' cardiorespiratory fitness, muscular fitness, and object control skills. This indicates that guided school-based physical activity programs can be influential in promoting physical fitness and motor competence among early adolescent students.