Background Chronically ill children are increasingly expected to join their peers in regular classrooms. However, sometimes schools do not provide adequate assistance. This study explores nursing teachers' thoughts and experiences on integrating such students into regular classrooms in Japan. Methods We analysed 79 essays written by nursing teachers collectively titled ‘The challenges of having chronically ill children in regular classrooms’. We conducted a qualitative study using Kinoshita's Modified Grounded Theory Approach. Results Nursing teachers identified three main obstacles: insufficient resources to support chronically ill students, parents not playing a supporting role in aiding them at school and a regular classroom not being suitable for them. However, collaborating with the children's medical staff proved successful at integrating them into regular classrooms. Conclusions Given these obstacles, it seems very difficult for nursing teachers to lead the way toward establishing cooperative support systems for the children. Instructions from medical staff could empower teachers to set up such systems.