This study explored a multidisciplinary approach for managing a Cleft Lip and Palate (CLP) patient with concurrent oral candidiasis. Prosthetic rehabilitation in a 74-year-old woman with CLP is a common congenital deformity. This case highlights the challenges and considerations in providing prosthetic treatment for patients with bone and tooth loss due to CLP, including the necessity of accounting for maxillary deformation and residual palatal defects. Interestingly, during the treatment process, a lesion was found in the rhinopharyngeal area, which was diagnosed as candidiasis caused by Candida albicans. The patient was successfully treated with nystatin, a mouthwash administered four times a day over a 14-day period. This case underscores the importance of comprehensive oral examinations in patients with CLP and the need for innovative clinical approaches to manage associated conditions such as candidiasis. This detailed case report highlights the nuanced treatment pathway for patients with CLP, emphasizing the importance of tailored prosthodontic strategies, interdisciplinary collaboration, and careful clinical observation.