This paper explores the dual institutions of charter schools and special education, and the unique issues that arise when an institution whose organizational structure is grounded in autonomy is forced to comply, by law, with significant regulatory demands. An understanding of the historical origins of each institution enables a thoughtful analysis of the observed challenges for charter schools in serving children with special needs in the present era, including legal constraints, enrollment practices, and funding disparities. Several successful organizational practices operating at this critical intersection are highlighted, and policy recommendations and directions for future research are discussed.