Background: Despite the benefits highlighted by motor interventions based on virtual reality for children with Developmental Coordination Disorder (DCD), there are still doubts whether these are greater than those obtained with conventional interventions due to the absence of systematized protocols and lack of evidence. Here we present a protocol to systematically compare the effects of two motor training programs (one Nintendo® Wii based and the other no-Wii motor activities) on the motor learning in children with DCD. Methods/Design: Two intervention protocols (one based on Nintendo® Wii and the other no-Wii motor activities) will be carried out, with interventions occurring twice a week in 60-minute sessions, with a minimum of 12 and a maximum of 16 sessions per child. The protocols were developed based on the domains of the Movement Assessment Battery for Children – Second Edition (MABC-2) (Manual dexterity, aiming & catching, balance), with two activities for each of the MABC -2 domains. The study will include children aged 7 to 10 with total MABC-2 score ≤16, and Developmental Coordination Disorder Questionnaire (DCDQ) score <46 (age of 7 years), score <55 (age group of 8 to 9 years and 11 months), or score <57 (age of 10 years) as scored by the parents. Children will be randomly allocated by draw in one of the two intervention protocols. MABC-2 and DCDQ will be applied before and after intervention to evaluate the effects of the interventions on motor performance and parents’ perception respectively. Motor learning will be assessed by means of the scores obtained in the games. Evaluators and therapists will be trained and evaluators will be blind about the data of the children in the study. Discussion: Owing to its motivating aspects, training with Nintendo® Wii may be particularly beneficial for children with DCD. The results of this study protocol will help researchers and therapists to better understand the benefits of Nintendo® Wii based motor intervention over those obtained with no-Wii interventions in children with DCD. It will also create references about more systematized protocols for replication in clinical practice, seeking the improvement of the motor components of these children. Trial registration: http://www.ensaiosclinicos.gov.br/rg/RBR-89ydgj/