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Cystic fibrosis transmembrane conductance regulator-related disorder (CFTR-RD) is an increasingly recognized genetic condition characterized by CFTR dysfunction without fulfilling the diagnostic criteria for cystic fibrosis. With the widespread application of genetic testing, an increasing number of patients with CFTR protein dysfunction have been identified; however, many do not meet the typical diagnostic criteria for cystic fibrosis. CFTR-RD may involve multiple organ systems and presents with heterogeneous and complex clinical manifestations, posing significant challenges for diagnosis and management. Here, we report the case of an adolescent male with bronchiectasis, elevated liver enzyme levels, and pancreatic exocrine insufficiency. Genetic analysis revealed a maternally inherited heterozygous intronic CFTR variant. Based on the clinical manifestations and laboratory findings, the patient was highly suspected of having CFTR-RD despite not fulfilling the diagnostic criteria for cystic fibrosis. This case underscores the importance of recognizing CFTR-RD in patients with multisystem involvement and atypical features of cystic fibrosis, and highlights the value of multidisciplinary evaluation in establishing an accurate diagnosis and developing an individualized treatment strategy.