The effectiveness of fundamental movement training interventions in adolescents is not fully understood. The Functional Movement Screen™ (FMS) may provide means of evaluating the effectiveness of such programs alongside traditional tests of physiological performance. Twenty-two children completed the FMS, plank, side plank, sit and reach and multi-stage fitness test. Participants were pair-matched by total FMS score and assigned to control or intervention. The intervention group received a weekly, 4 x 30-min training sessions with an emphasis on movement quality while the control group were involved in generic multi-sport activity.. A smallest-worthwhile effect of 0.2 between participants SDs was set a priori for all measures except total FMS score for which a change of 1 unit was chosen. When compared to the control our intervention had a likely trivial effect for FMS score (0.2 AU; 90% confidence limits ±1.2 AU), a very likely small beneficial effect for plank score (87%; ±55%) but a possibly small harmful effect for side plank score (-22%; ±49%). A likely trivial effect was observed for the sit and reach test (0.3%; ±15%) while the effect of the training intervention on predicted VO2max was unclear (-0.3%; ±11%). Unexpectedly, generic multi-sport activity enhanced both side plank and sit and reach test performance in the control group. These results demonstrated that short-term interventions might affect specific isolated components of fitness but not FMS performance.