Purpose: Epithelial–mesenchymal transition (EMT) is an important characteristic in the remodelling of chronic rhinosinusitis with nasal polyps (CRSwNP). IL‐36γ and fibroblast activation protein (FAP) may exacerbate remodelling in CRS. Here, we aimed to determine whether IL‐36γ and FAP expression are associated with EMT and may be a predictor for CRSwNP prognosis. Methods: Fifty‐two non‐Eos CRSwNP patients and 12 control patients were obtained and were followed up for more than 1 year after surgery. IL‐36γ, FAP and EMT markers expression were evaluated by real‐time polymerase chain reaction and western blot. Masson trichrome staining was adopted to assess tissue fibrotic changes. Furthermore, the soluble form of IL‐36γ and FAP in nasal secretions was detected by ELISA. Results: While basal expression of E‐cadherin decreased, the expression of IL‐36γ, vimentin and FAP increased in nasal polyps. In well‐prognosis patients, the expression of IL‐36γ, vimentin and FAP were significantly decreased than in poor‐prognosis patients, while the protein expression of E‐cadherin was increased. The protein expression of IL‐36γ was notably increased in recurrent nasal polyps than in preoperation specimens. A positive relationship between IL‐36γ and FAP expression, a negative relationship between IL‐36γ and E‐cad expression was noted. The soluble form of IL‐36γ and FAP increased during the development of non‐Eos CRSwNP, with the highest level in poor‐prognosis patients after surgery. Conclusion: Non‐Eos CRSwNP have partially undergone EMT under baseline conditions. IL‐36γ and FAP expression were related with EMT, the soluble form of IL‐36γ and FAP in nasal secretions may predict the prognosis of patients.