The birth of a child with congenital malformation and serious illness impacts the experiences of all family members and the educational process, but there are only rare descriptions of such cases in the literature. The aim of this study is to understand better the lived experiences of a Czech family who have a child with congenital malformations with a focus on his education in an inclusive environment. The study is based on van Manen’s methodology and autobiographic (or semi-structured) interviews with Karl (19), his mother (46), and his father (49). Data were analyzed for every participant separately: the mother—repeated challenges associated with increasing new health complications, discomfort of son, school support, the future, optimism, and gratefulness; the father—comprehensive support of the son, including all family; Karl—concealment of disability, difficulties associated with disability, participation, school support, relationship with peers, and the future. Based on the results of this case study, for the education of students with congenital malformation and illness, we recommend including parents, healthcare professionals, and school staff in the mutual teamwork; adapting the timetables and spatial arrangements at school; and coordinating the educational process with necessary interventions.