Children with Developmental Coordination Disorder (DCD) experience motor competence challenges that hinder their participation in physical activities and affect daily functioning. While traditional motor skills training is commonly used, sport-based interventions offer the potential for greater benefits by providing dynamic, contextually rich environments for learning. This study aimed to evaluate the effectiveness of mini-handball training versus conventional motor skills training in improving coordination in children with DCD. Methods: Forty-four children aged 9–10 years from Khorezm, Uzbekistan, with coordination difficulties (scores below the 16th percentile in the MABC-2) were randomly assigned to three groups: mini-handball training (n = 15), motor skills training (n = 15), and control (n = 14). Both intervention groups participated in three 90 min sessions per week for 12 weeks. The mini-handball group engaged in sport-specific drills including passing, dribbling, shooting, and small-sided games, while the motor skills group performed balance, locomotor, and fine motor exercises. Pre- and post-intervention assessments were conducted using the MABC-2. Data were analyzed using linear mixed models with time, group, and their interaction as fixed effects. Results: Both intervention groups demonstrated significant improvements in motor coordination compared to controls. However, in general, the mini-handball group outperformed the other groups, particularly in domains requiring anticipatory control and visuomotor integration, including aiming and catching, balance, and overall coordination scores. Conclusions: Mini-handball represents a promising, ecologically valid intervention for children with DCD. By integrating motor skills practice with cognitive challenge, social interaction, and intrinsic motivation within a meaningful sport context, mini-handball appears more effective than traditional training approaches. These findings suggest that sport-based, open-skill interventions should be considered in therapeutic protocols, school curricula, and community programs for children with DCD. Future research should examine long-term retention, transfer to daily activities, and implementation across diverse populations.