Background Special educational needs (SEN) provision is designed to help pupils with additional educational, behavioural or health needs; for example, pupils with cleft lip and/or palate may be offered SEN provision to improve their speech and language skills. Our aim is to contribute to the literature and assess the impact of SEN provision on health and educational outcomes for a well-defined population. Methods We will use the ECHILD database, which links educational and health records across England. Our target population consists of children identified within ECHILD to have a specific congenital anomaly: isolated cleft lip and/or palate. We will apply a trial emulation framework to reduce biases in design and analysis of observational data to investigate the causal impact of SEN provision (including none) by the start of compulsory education (Year One – age five year on entry) on the number of unplanned hospital utilisation and school absences by the end of primary education (Year Six – age ten/eleven). We will use propensity score-based estimators (inverse probability weighting (IPW) and IPW regression adjustment IPW) to compare categories of SEN provision in terms of these outcomes and to triangulate results obtained using complementary estimation methods (Naïve estimator, multivariable regression, parametric g-formula, and if possible, instrumental variables), targeting a variety of causal contrasts (average treatment effect/in the treated/in the not treated) of SEN provision. Conclusions This study will evaluate the impact of reasonable adjustments at the start of compulsory education on health and educational outcomes in the isolated cleft lip and palate population by triangulating complementary methods under a target-trial framework.