Background: The survival of non-small cell lung cancer (NSCLC) patients with brain metastases is reported to be 3~6 months even with aggressive treatment. Some patients have very short survival after aggressive treatment and reliable prognostic scoring systems for patients with cancer have a strong correlation with outcome, often supporting decision making and treatment recommendations. Methods: A total of one hundred twenty two NSCLC patients with brain metastases who received gamma knife radiosurgery (GKRS) were analyzed. Survival analysis was calculated in all patients for thirteen available prognostic factors and four prognostic scoring systems: score index for radiosurgery (SIR), recursive partitioning analysis (RPA), graded prognostic assessment (GPA), and basic score for brain metastases (BSBM). Results: Age, Karnofsky performance status, largest brain lesion volume, systemic chemotherapy, primary tumor control, and medication of epidermal growth factor receptor tyrosine kinase inhibitor were statistically independent prognostic factors for survival. A multivariate model of SIR and RPA identified significant differences between each group of scores. We found that three-tiered indices such as SIR and RPA are more useful than four-tiered scoring systems (GPA and BSBM). Conclusion: There is little value of RPA class III (most unfavorable group) for the same results of 6-month and 1-year survival rate. Thus, SIR is the most useful index to sort out patients with poorer prognosis. Further prospective trials should be performed to develop a new molecular- and gene-based prognostic index model.