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Background The presence of EGFR mutation in patients with advanced non‐small cell lung cancer (NSCLC) plays an important role in determining the appropriate treatment, response, and survival. Therefore, this study attempted to predict the prognosis of NSCLC patients using data from quantitative mutation measurements. Methods The data of patients with advanced NSCLC who underwent EGFR mutation testing using the peptide nucleic acid (PNA) mediated clamping method at the Pusan National University Hospital from October 2015 to December 2017 were retrospectively analyzed. The efficiency of PNA clamping was determined by measuring the threshold cycle (Ct) value. The ΔCt−1 value (standard Ct value minus sample Ct value) was calculated to quantify EGFR mutation. Results During the study period, 71 patients were treated with EGFR‐tyrosine kinase inhibitors. The cutoff point for the ΔCt−1 value derived from the receiver operating characteristic curve was 5.32. A survival benefit was observed in the group with an ΔCt−1 value > 5.32 or with a common EGFR mutation type compared to the group with an ΔCt−1 value < 5.32. Conclusion EGFR mutation testing using PNA clamping may predict patient survival, especially in patients with common EGFR mutations, such as exon 19 deletion or L858R. A higher ΔCt−1 value correlates with better survival.