School refusal among neurodivergent students underscores systemic failures in traditional educational systems. This qualitative study, informed by the neurodiversity paradigm, examines how Flexible Learning Options (FLOs) in South Australia address drivers of disengagement, such as sensory overload, punitive discipline, and identity erasure, while fostering reengagement through autonomy, relational safety, and identity empowerment. Drawing on interviews conducted with a subsample of 18 students aged 13–19, reflexive thematic analysis resulted in the development of three themes: (1) autonomy and its limits, (2) relational safety as harm reduction, and (3) identity empowerment through neuroaffirmation. The findings reported in this paper advocate for educational models that transform flexibility from a temporary solution into a blueprint for equity, ensuring schools become spaces of support rather than harm for neurodivergent learners.