Background: Uncommon epidermal growth factor receptor (EGFR) mutations are a heterogeneous population of molecular alterations, and clinical data on the outcomes of afatinib in patients with non-small cell lung cancer (NSCLC) harboring uncommon EGFR mutations are limited. The purpose of this pooled analysis was to investigate the clinicopathological features of uncommon EGFR mutations in patients and the treatment response and survival associated with afatinib treatment.Methods: We performed a literature search in the NCBI PubMed database to identify relevant articles and completed a pooled analysis based on 37 related published studies.The relationship between clinical characteristics, EGFR mutation type and treatment response were analyzed using univariate chi-square analysis, and survival analysis was performed using the Kaplan–Meier method.Results: A total of 57 patients were included in this pooled analysis. The objective response rate to treatment with afatinib was 46.4%, with a median PFS of 7.0 months.Patients with a single uncommon EGFR mutation are more likely than patients with multiple mutations to show a good tumor response after receiving afatinib (ORR: 57.9% vs 26.3%, HR: 0.260, 95% CI: 0.078-0.869, p=0.029). Similarly, patients with a single uncommon EGFR mutation had a longer PFS than patients with multiple mutations (mPFS: 10.0 months vs 3.6 months, HR: 2.906, 95% CI: 1.496-5.646, p=0.002). In addition, for patients with a good treatment response, the PFS was also longer (HR: 2.902, 95% CI: 1.522-5.533, p=0.001).Conclusions: For patients with uncommon mutations, the outcomes of afatinib is worse than that of patients with classic sensitive mutations but higher than that of EGFR wild-type patients. Uncommon EGFR mutations contain various subtypes, and different subtypes have different sensitivities to afatinib. Patients with a single rare mutation show better treatment responses to afatinib and better prognoses than patients with multiple mutations.