Congenital heart disease (CHD) has effects on growth and development. However, information on how the structure of the mandibular bone is affected is limited. In the present study, we aim to compare mandibular bone structures of children affected with CHD and healthy ones through the fractal analysis method and radiomorphometric indices based on panoramic radiographs. The study consisted of 80 children (20 with cyanotic CHD, 20 with acyanotic CHD, 40 control) who were diagnosed with CHD and were treated through interventional therapy or followed up through medical therapy. Fractal dimension (FD) was performed in three different areas (angulus, corpus, and interdental bone) on 80 panoramic radiographs. Additionally, we assessed various radiomorphometric indices: mandibular cortical width (MCW), panoramic mandibular index (PMI), mandibular cortical index (MCI), and simple visual estimation (SVE). p < 0.05 was accepted as statistically significant in the analysis. Values of mean MCW, PMI, MCI, SVE, and FD measurements in children affected with CHD were found to be similar to the control group, regardless of whether they were cyanotic or acyanotic (p > 0.05). In this study, fractal analysis and radiomorphometric indices revealed no trabecular structure and mineral density changes in mandibular bone of children and adolescents with CHD compared to healthy subjects.