Thousands of children with cancer participate in medical and social sciences research during and beyond their hospitalization and treatment. However, methodological techniques and issues in conducting qualitative research with children with cancer have received little attention in the literature to date. Therefore, the present article explores the methodological negotiations made when conducting a phenomenological study of the school experiences of children with cancer. While conducting semi-structured interviews with 10 participants who were 6 to 12 years old, the following areas of methodological concern arose: (1) navigating the demands of illness, treatment, and hospitalization, (2) developing relationships with participants/parents/researcher, and (3) interpreting children's words and cues. Future qualitative research with children with cancer should incorporate flexible design, reflexive interpersonal engagements, and child-friendly and familiar data collection methods to minimize the burden of research participation. These considerations also extend to inform qualitative research with children diagnosed with other chronic illnesses in various social settings.