This study aimed to investigate dental treatment patterns in pediatric patients with rare diseases at Yonsei University Dental Hospital over 3 years. Data of 786 pediatric patients diagnosed with rare diseases who received dental treatment between January 2020 and December 2022 were analyzed retrospectively. Patients were identified through electronic medical record screening for rare disease codes registered with the Korea Disease Control and Prevention Agency. Demographics, rare disease categories, and dental treatment methods and modalities were analyzed using chi-square tests, Fisher’s exact tests, t-tests, and logistic regression. Significant differences in dental treatment needs and methods were observed among categories. Patients with nervous system diseases were less likely to receive preventive or restorative treatments, such as sealants (<i>p</i> = 0.0062) and composite restoration (<i>p</i> = 0.0171), and had a higher prevalence of disabilities (<i>p</i> < 0.00001), leading to greater dental care challenges. Conversely, patients with congenital malformations required more extensive treatments, including stainless-steel crowns (<i>p</i> = 0.0118) and surgery (<i>p</i> = 0.0234), often under general anesthesia (<i>p</i> = 0.0337). The study underscores the importance of tailored dental care protocols and interdisciplinary collaboration to address the needs of pediatric patients with rare diseases, enhancing their oral health outcomes and quality of life.