The major purpose of this study was to examine the effects of a jump rope-based physical activity afterschool program on middle school students’ physical fitness. Sixty students (Mage = 13.37, SD = 0.58; 53.3% female) participated in a 12-week jump rope-based afterschool program (45 min/time, three times/week). Participants were randomly assigned to three groups: (a) freestyle rope skipping (N = 20), traditional jump rope (N = 20), and a control group (N = 20). Physical fitness tests, including muscular strength (standing long jump, right-hand grip, and left-hand grip), flexibility, body composition, and bone mineral density (BMD) were measured in pre- and post-tests. A 2 (time) × 3 (groups) repeated measure multivariate analysis of variance (MANOVA) was performed. The results found significant improvements in muscular strength (standing long jump, right-hand grip, and left-hand grip) in both intervention groups (p < 0.001; ds = 0.2–0.44). Only the freestyle rope skipping group had increased BMD (p < 0.05, d = 0.33). Compared to the traditional jump rope, the freestyle rope skipping group showed significantly higher improvement in flexibility (p < 0.05, d = 0.83). These findings suggest that the jump rope-based afterschool program with freestyle rope skipping would be more effective than traditional jump rope to promote physical fitness performance among adolescents.