The activation of Janus kinase 1 (JAK1) has been reported to occur in non-small cell lung cancer (NSCLC), activating the JAK/signal transducers and activators of transcription cascade. However, the association between JAK1 activation and the prognostic value in NSCLC remains unclear. The present study initially investigated the association between expression of the activated form of JAK1 (p-JAK1) and prognosis in patients with NSCLC. A cohort of 142 resected primary NSCLC tissue samples, including 74 adenocarcinoma (ADCC) and 68 squamous cell carcinoma samples, were analyzed. p-JAK1 expression status was determined by immunohistochemistry. Evaluation of epidermal growth factor receptor (EGFR) gene amplification by fluorescence in situ hybridization was subsequently performed in 74 ADCC samples. The prognostic significance of p-JAK1 expression and EGFR gene amplification were evaluated with univariate and multivariate survival analyses. Compared with normal lung tissue, p-JAK1 expression level was significantly increased in NSCLC (P<0.001). Positive p-JAK1 expression indicated a poor prognosis, particularly for patients in early stages (stage I/II, including tumor size <3 cm, Lymph node invasion N0/1; all P<0.05). p-JAK1 expression was an independent predictor of a poor prognosis (P=0.022). The overall survival time for patients with positive p-JAK1 expression and EGFR-amplified tumors was significantly shortened compared with patients with tumors negative for one or both features (both features present vs. neither feature present, P<0.001). The results provided clinical evidence that the activation of JAK1 was an independent prognostic factor, particularly in early stage NSCLC. The combination of EGFR gene amplification and p-JAK1 expression may be a novel target for the selection of individual therapy strategies and predicting the effects of therapy for NSCLC.