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Introduction Children diagnosed with developmental coordination disorder (DCD) exhibit a range of challenges in both gross and fine motor skills, characterised by sluggish and awkward movements. Additionally, they experience deficits in balance and coordination. Without appropriate intervention, these difficulties may endure into adolescence and adulthood, impacting various facets of their daily lives, including learning, social interactions and recreational activities.Methods and analysis Employing a randomised controlled trial design, 60 children diagnosed with DCD will be randomly assigned to two groups. The experimental group will receive Baduanjin training in addition to health education, while the control group will undergo health education alone. Following an 8-week intervention period, assessments using motor assessment battery for children-second edition, ProKin 254 Balance Test System will be conducted to evaluate the impact of Baduanjin on the motor coordination and balance in children with DCD. Furthermore, functional near-infrared spectroscopy will be employed to capture haemodynamic data from the children’s brain movement-related cortex during functional activities. These data will be analysed to assess the level of cortical activation, strength of functional connectivity and their correlation with changes in motor function, with the goal of investigating the cerebral blood oxygenation mechanisms underlying the effectiveness of the Baduanjin intervention.Ethics and dissemination This study has been submitted for approval and has received ethical clearance from the Medical Ethics Committee of Shanghai Fourth People’s Hospital (2023080-001). The results of the study will be published in a peer-reviewed scientific journal.Trial registration number ChiCTR2300078980.