Background: Conclusive evidence supports the importance of fundamental movement skills (FMS) proficiency in promoting physical activity and countering obesity. In children with Down Syndrome (DS), FMS development is delayed, which has been suggested to be associated with balance deficits. This study therefore examined the relationship between FMS proficiency and balance ability in children with DS, with the aim of contributing evidence to programmes that address FMS delay. Methods: Participants consisted of 20 children with DS (7.1 ± 2.9 years old) and an age-matched control group of children with typical development (7.25 ± 2.5 years). In the first part of the study, FMS (i.e. locomotor and object control) proficiency of the children was tested using the Test of Gross Motor Development-2. Balance ability was assessed using a force platform to measure centre of pressure average velocity (AV; mm/sec), path length (mm), medio-lateral standard deviation (mm) and antero-posterior standard deviation (mm). In the second part of the study, children with DS participated in 5 weeks of FMS training. FMS proficiency and balance ability were tested post-training and compared to pre-training scores. Verbal and visuo-spatial short-term memory capacities were measured at pre-training to verify the role of working memory in skill learning. Results: FMS proficiency was associated with centre of pressure parameters in children with DS but not in children with typical development. After controlling for age, AV was found to predict significant variance in locomotor (R[superscript 2] = 0.61, P < 0.001) and object control (R[superscript 2] = 0.69, P < 0.001) scores. FMS proficiency and mastery improved after FMS training, as did AV, path length and antero-posterior standard deviation (all P < 0.05). Verbal and visuo-spatial short-term memory did not interact with the effects of training. Conclusions: Children with DS who have better balance ability tend to have more proficient FMS. Skill-specific training improved not only FMS sub-skills but static balance stability as well. Working memory did not play a role in the changes caused by skills training. Future research should examine the causal relationship between balance and FMS.