Children with special educational needs (SEN) are a diverse group facing numerous challenges related to well‐being and mental health. Understanding the predictors of well‐being in this population requires the incorporation of diverse factors along with approaches that can uncover complexity in how these factors work together to influence well‐being. We longitudinally predicted subjective well‐being in a group of children with diverse special educational needs (N = 499; M = 8.4 ± 0.9 years). Thirty‐two variables ‐ ranging from demographics to various categories of life experiences ‐ were used as predictors for both nonlinear machine learning and classical linear classifiers. Nonlinear machine learning classifiers exhibited much performance in predicting subjective well‐being (F1 score = 0.72 to 0.84) compared to traditional linear classifiers. Overall, across all children, prior subjective well‐being, numeracy, literacy skills, and interpersonal dimensions played important roles. However, clustering further identified four distinct clusters sharing important predictors: a ‘socializer’ cluster dominated by interpersonal functioning predictors, an ‘analyzer’ cluster emphasizing academic skills predictors, and two clusters with more diverse sets of important predictors. Our research highlights the multiple pathways toward well‐being in children with SEN as uncovered by machine learning, with implications for understanding and supporting their well‐being.