This report describes a case of an 11‐year‐old Chinese boy with cystic fibrosis (CF) bearing the c.1521_1523delCTT/c.3874‐4522A>G genotype, an extremely rare CF genotype in the Chinese population. Notably, the deep intron mutation c.3874‐4522A>G, which has mainly been reported in patients with phenotypically mild CF, is identified here for the first time in a Chinese patient with severe CF. In the case discussed here, the c.3874‐4522A>G mutation was associated with severe pulmonary disease with early symptoms onset, progressive bronchiectasis, recurrent airway infection with both Pseudomonas aeruginosa and methicillin‐resistant Staphylococcus aureus, rapid decline of lung function and poor weight gain. Despite intensive hospital‐based pulmonary care and optimized therapy, the child died of cardiopulmonary failure 3 months after discharge.