This study aimed to identify the influence of illness cognition and background factors on the sense of coherence among junior high school and high school students with congenital cardiac disease. We conducted an examination using the illness cognition scale and sense-of-coherence scale, and verified the reliability and validity of both. Participants were 172 students with congenital cardiac disease and 295 healthy students, who were 12–18 years old. The relationship among sense of coherence, basic and disease-related attributes, and illness cognition in healthy adolescents and those with congenital cardiac disease was investigated. Sense of coherence was higher in boys than in girls and higher in junior high students than in high school students. Adolescents with congenital cardiac disease scored higher for sense of coherence than healthy students. Those who scored lower on the illness cognition scale for “hardships resulting from restrictions and limitations for illness”, “the desire to be understood by others”, “anxieties about the state of the disease and possibility of death”, or “not wanting people to know of one’s disease” showed higher sense of coherence than those who had higher scores for these elements.