Understanding the stability of individual differences in motor performance during the early years of life, despite normative age-related growth in motor performance, has important implications for identification of motor coordination difficulties and subsequently, early remediation. Therefore, the aims of the present study were to examine the degree of rank-order and individual-level stability in motor performance in young children with different levels of motor skill proficiency. Subsequently, we explored the influence of child variables (i.e., age, gender, and behavioural self-regulation) on different aspects of stability. In this longitudinal study, a community sample of 68 participants (49% girls) with a mean age of 3 years and 11 months (SD = 7 months) were assesses in three six-monthly waves. The total standard score of the Movement Assessment Battery for Children-2 (MABC-2) was used as the measure of motor performance. Rank-order stability was examined with zero-order Pearson correlations. Individual-level stability was examined by means of stability in classifications (at risk for motor coordination difficulties versus typically developing). In addition to examining stability in group classification, the Reliable Change Index (RCI) was calculated to examine if the difference in a child's scores over time exceeded (increased or decreased relative to) the expected change. The results showed moderate to high rank-order stability between time points. No significant differences in degree of rank-order stability were found between boys and girls and between 3-year old and 4-year old children. In terms of stability of classification, it was shown that for ~50% of the children with motor coordination difficulties and ~ 90% of typically developing the classification based on the cut-off score on the MABC-2 was stable. Based on the RCI, over 90% showed individual-level stability. The level of behavioural self-regulation at T1 (as measured with the Head-Toes-Knees-Shoulders task) was not significantly related to individual-level stability in motor performance. In conclusion, our findings highlight the importance of a careful choice of stability measures and a reflection on the implications of their results. More research is needed to understand which child and environmental variables impact on stability.