Background The number of children with complex medical conditions has increased in recent decades. In this context, a complex chronic condition is characterized by multiple morbidities that require intensive or continuous health care according to the level of severity. Given their various health conditions, it is challenging to provide special education to these children, but there is still insufficient evidence regarding the practical experiences of educators. The aim of this study was to investigate special education teacher’s perceptions, experiences, and challenges while developing interpersonal relationships and communicating with children who have complex chronic conditions. Methods We recruited and interviewed 21 special education school teachers in Japan. The transcripts of the interviews were analyzed using thematic analysis. Results Our analysis revealed four themes, including “searching for the meaning,” “complex chronic conditions as a difficult reality,” “widening experience for the future,” and “priority for interacting with children.” These themes reflect the perceptions, experiences, and challenges of the special education teachers. Conclusions In cases where children have severe functional limitations, it is more challenging to understand child-teacher interactions. This highlights the importance of searching for meaning in educational practices used among children with complex chronic conditions. Our findings may provide helpful insight into the experiences and challenges faced by special educators who engage with these children.