The average levels of physical activity in children are below the ideal, which may influence children's health and motor competence levels. Therefore, this study aimed to assess the impact of a 10-week play-based after-school program on 50 twelve-year-old students’ anthropometric characteristics (body height and body weight), coordinative abilities (flamingo balance test and T-test agility), and physical fitness (sit and reach, 20-m sprint test, SLJ, CMJ, and handgrip). After baseline assessments, the students were randomly divided into two groups: one participating in a play-based after-school program (experimental group) and the other attending regular PE classes (control group). No differences were noted between the sexes. Analysis revealed baseline differences between groups in body weight, agility T-test, and right-handgrip, with no significant sex differences. Following the intervention, the experimental group demonstrated improvements in the 20-m sprint test (F(1,46) = 11.03, p < 0.01), flamingo balance test (F(1,46) = 9.16, p = 0.004), SLJ (F(1,46) = 5.30, p = 0.03), agility T-test (F(1,46) = 28.30, p < 0.01), and right-handgrip (F(1,46) = 6.59, p < 0.01). In summary, the results suggested that a 10-week play-based after-school program enhances coordinative abilities and physical fitness in 12-year-old children. This underscores the potential advantages of integrating play-based physical activities into schools to promote holistic health and fitness in children.