Despite intensified interest in secondary school applications of Response-to-Intervention (RtI), research in this area remains sparse. This study utilized a qualitative focus group methodology to explore special education directors’ perceptions of current barriers, facilitators, roles, and practices related to RtI implementation in secondary settings. Based on their unique potential to affect change and promote collaboration between general and special educators, special education directors were selected as participants. Across two focus groups, four themes emerged: systems structures, roles and attitudes, evidence-based practices, and training and professional development needs. Each theme is explored in depth, followed by practical implications, limitations, and recommendations for practice. Although numerous barriers emerged, they should be viewed not as limitations to RtI in secondary schools but rather as serving to identify the systemic factors needed to support the complexity of an RtI initiative beyond the elementary school years.