Special education in the United States has been historically problematic for several reasons, and limited research has been conducted to examine the close connection between teachers’ experiences in the classroom (both general and special education teachers) and principals’ leadership. Teacher perceptions have a great impact on the learning of special education students, and how teachers perceive principals’ effectiveness in their leadership determines how teachers can help these students learn better. Therefore, I conducted a mixed-methods study to learn more about teachers’ perceptions of principals’ emotional intelligence (EI) and agency. I administered a survey to Kindergarten through Grade 5 general and special education teachers across 16 suburban public elementary schools to collect quantitative data that allowed participants to then opt in for qualitative individual interviews. The survey yielded a 42.14% response rate, and nine teachers were interviewed. Structure-agency theory and EI competencies informed the analysis of these elementary school teachers’ perceptions of principals’ EI and perceived agency within the structures of special education. Overall, the teachers in this study had positive perceptions of principals’ EI across special education structures. However, teachers perceived principals’ EI differently, depending on the structure of special education and EI competencies. School principals’ understanding of how teachers perceived the roles of principals in framing and working within special education contributes to a greater understanding of how principal agency is perceived. Principals can be informed on how to improve their practices as instructional leaders, specifically for students receiving special education services. Thus, this study informs professional learning and strategic planning, and inspires principals to learn more about EI and agency in their current working structures.