Background Proficiency in fundamental movement skills (FMS) lays the foundation for being physically active and developing more complex motor skills. Improving these motor skills may provide enhanced opportunities for the development of a variety of perceptual, social, and cognitive skills. Objective The objective of this systematic review and meta-analysis was to assess the effects of FMS interventions on actual FMS, targeting typically developing young children. Method Searches in seven databases (CINAHL, Embase, MEDLINE, PsycINFO, PubMed, Scopus, Web of Science) up to August 2015 were completed. Trials with children (aged 2–6 years) in childcare or kindergarten settings that applied FMS-enhancing intervention programs of at least 4 weeks and meeting the inclusion criteria were included. Standardized data extraction forms were used. Risk of bias was assessed using a standard scoring scheme (Effective Public Health Practice Project—Quality Assessment Tool for Quantitative Studies EPHPP). We calculated effects on overall FMS, object control and locomotor subscales (OCS and LMS) by weighted standardized mean differences (SMD between ) using random-effects models. Certainty in training effects was evaluated using GRADE (Grading of Recommendations Assessment, Development, and Evaluation System). Results Thirty trials (15 randomized controlled trials and 15 controlled trials) involving 6126 preschoolers (aged 3.3–5.5 years) revealed significant differences among groups in favor of the intervention group (INT) with small-to-large effects on overall FMS (SMD between 0.46), OCS (SMD between 1.36), and LMS (SMD between 0.94). Our certainty in the treatment estimates based on GRADE is very low. Conclusions Although there is relevant effectiveness of programs to improve FMS proficiency in healthy young children, they need to be interpreted with care as they are based on low-quality evidence and immediate post-intervention effects without long-term follow-up.