Background: Motor development of many children in rural areas of South Africa is compromised because of various socio-economic factors, hence, the need to address these developmental needs. Aim: To examine the immediate and sustainable effects of a 9-week movement programme on fundamental movement skills (FMS) of school children. Setting: Seven to eight years old school children in Raymond Mhlaba Municipality, Eastern Cape province. Methods: A two-group, pre-post-re-test research design was used. Fundamental movement skills (FMS) proficiency was assessed using the Test of Gross Motor Development-Third Edition (TGMD-3) at pre-test, post-test and re-test after 6 months. Ninety-three school children (intervention group [IG] = 57) and (control group = 36), with a mean age of 7.12 (± 0.71) participated in the study. The twice-a-week FMS programme of 30 min was conducted during school hours. Statistical analysis included an ANOVA type of hierarchical linear model (HLM) (mixed models) procedure to test for intervention effects with school, time, sex and group as covariants. Cohen's effect size was calculated to assess the practical significance of changes. Results: Immediate and sustainable effects were found on locomotor (p < 0.05; d > 1.7, p < 0.05; d > 2.0), ball skills (p < 0.05; d > 0.7, p < 0.05; d > 1.5) and the gross motor index (GMI) of the IG (p < 0.05; d > 1.0, p < 0.05; d > 2.0). Conclusions: A short-duration FMS intervention significantly improve locomotor, ball skills, and GMI of school children in rural areas. Contributions: Interventions of this nature are encouraged to improve the FMS development of school children, especially in rural areas, as it can enhance the building blocks required in the future development of these children.