School readiness of children with special educational needs (SEN) is still understudied. The present study examined how the presumed bidirectional relationship between impaired academic performance (AP) and internalising problems (IP) could be favourably influenced. In this regard, it was assumed that children’s adaptive emotion regulation plays a crucial role, as it was shown to be independently related to improved AP and fewer IP. However, to gain stronger evidence for this assumption, it should be further clarified whether adaptive emotion regulation, AP and IP are also jointly associated and, if so, how this is reflected in children with SEN. To explore these issues, two different models were tested in a cross-sectional pilot including 61 Flemish elementary school children with SEN (39 boys and 22 girls, mean age = 10.0 years old). Teachers reported on adaptive emotion regulation, AP and IP. The results indicated that AP partially mediated the relationship between adaptive emotion regulation and IP (model 1), while IP fully mediated the relationship between adaptive emotion regulation and AP (model 2). Practical implications, strengths, and limitations were discussed.