The aim of this study was to examine differences in the performance of children with probable Developmental Coordination Disorder (p-DCD) and balance problems (BP) and typical developing children (TD) on a Wii Fit task and to measure the effect on balance skills after a Wii Fit intervention. Twenty-eight children with BP and 20 TD-children participated in the study. Motor performance was assessed with the Movement Assessment Battery for Children (MABC2), three subtests of the Bruininks Oseretsky Test (BOT2): Bilateral Coordination, Balance and Running Speed & Agility, and a Wii Fit ski slalom test. The TD children and half of the children in the BP group were tested before and after a 6 weeks non-intervention period. All children with BP received 6 weeks of Wii Fit intervention (with games other than the ski game) and were tested before and afterwards. Children with BP were less proficient than TD children in playing the Wii Fit ski slalom game. Training with the Wii Fit improved their motor performance. The improvement was significantly larger after intervention than after a period of non-intervention. Therefore the change cannot solely be attributed to spontaneous development or test–retest effect. Nearly all children enjoyed participation during the 6 weeks of intervention. Our study shows that Wii Fit intervention is effective and is potentially a method to support treatment of (dynamic) balance control problems in children.