Background: Inter-limb asymmetry above a certain threshold in functional performance indicates increased injury risk in sports. Fatigue has been found to increase bilateral asymmetry in lower-limb jumping performance among high-school and adult athletes, whereas this impact has not been examined for child athletes. Methods: Performance of single-leg jumps, Star Excursion Balance Test (SEBT), and muscle (hamstring and gastrocnemius) flexibility were measured for 13 elite male child Taekwondo athletes (aged 9.85 ± 0.80 years) at both the rested and fatigued states to examine the inter-limb asymmetry. A two-way repeated measures ANOVA was conducted to examine for difference for each test and the interaction between limb (dominant, non-dominant leg) and state (rested, fatigued state). Paired t test or Wilcoxon Signed-Rank test was used to compare the asymmetry magnitude at the rested vs. fatigued state for each test, and the variation in performance post fatigue in the dominant vs. non-dominant leg when appropriate. Results: The inter-limb asymmetry in triple-hop distance significantly (p = 0.046) increased with fatigue, whereas the asymmetry significantly (p = 0.004) decreased with fatigue in anterior (ANT) reach distance in SEBT. A significant (p = 0.027) limb by state interaction was shown for posterolateral (PL) reach distance in SEBT, wherein a significant (p = 0.005) bilateral difference was only shown at the rested state. The PL reach distance showed a significantly greater decrease (p = 0.028) post fatigue when using the dominant leg for support compared to using the non-dominant leg.Conclusion: Fatigue significantly impacts inter-limb asymmetry in jump performances and dynamic balance for child athletes, while the variation in inter-limb asymmetry post fatigue may be different across tests. For the purpose of injury prevention, practitioners should consider assessing the inter-limb asymmetry for children at both the rested and fatigued state, and be mindful of the fatigue response of each leg in functional tests.