Health-related physical fitness is an important risk factor of cardiovascular disease. While previous studies have identified children with developmental coordination disorder (DCD) to be less physically fit than typically developing (TD) peers, there is limited longitudinal research in this area. This study was undertaken to evaluate concomitant changes in motor coordination and health-related physical fitness of Taiwanese children with and without DCD over a three-year period. The Movement Assessment Battery for Children (Movement ABC) test was used to evaluate motor coordination, while health-related physical fitness included several core components: (1) body mass index (BMI), (2) sit and reach forward, (3) long jump, (4) sit-ups, and (5) 800-m run. Both the Movement ABC and fitness tests were implemented once each a year for three years. Twenty-five children with DCD and 25 TD children, matched by age and gender participated in this study. The TD group showed significant long-term changes in BMI and long jump while the DCD group showed significant increases in BMI values and decreases in flexibility, measured by the sit and reach task. In general, children with DCD performed worse on the items of flexibility, muscle strength and muscle endurance after the first year. Compared to age- and gender-matched norms, children with DCD not only were less physically fit, but showed a significant long-term decline in flexibility and abdominal or core strength (sit-ups). In years two and three, there was a significant negative correlation between poor fitness and motor coordination. Based on the results of this longitudinal study, greater attention should be paid to monitoring and improving physical fitness of children with DCD to prevent further health-related problems while intervention.