Purpose Dual-time-point (DTP) FDG PET/CT has been shown to be useful for lymph node (LN) staging in patients with non-small-cell lung cancer (NSCLC). The aim of this study was to evaluate the LN staging ability of DTP FDG PET/CT in the predominant area of pulmonary tuberculosis. Methods Sixty-nine NSCLC patients underwent DTP PET/CT. Regions of interest were placed on each LN of each station, and the maximum SUVs were measured. Three variables were obtained: (1) the SUV on the early scan ($SUV_{early}$), (2) the SUV on the delayed scan ($SUV_{delayed}$), and (3) the retention index of the SUV (RI). Each patient had one final LN stage and three other LN stages according to the cutoff values of $SUV_{early}$, $SUV_{delayed}$, and RI. Results In the LN-based analysis, the area under the ROC curve of $SUV_{delayed}$ (0.884) was significantly larger (P< 0.01) than those of $SUV_{early}$ (0.868) and RI (0.717). Among the three variables, $SUV_{delayed}$ was more accurate (P<0.01) for detecting the mediastinal LN metastasis than $SUV_{early}$ and RI. In the patient-based analysis, $SUV_{delayed}$ had correctly determined LN stages in 55 of 69 patients (sensitivity, specificity, and accuracy=88.7 %, 50.0 %, and 79.7 %), whereas $SUV_{early}$ and RI correctly determined LN stages in 53 and 52 patients, respectively. Conclusions In this study, comparing the diagnostic efficacy of $SUV_{early}$, $SUV_{delayed}$, and RI for LN staging in patients with NSCLC, $SUV_{delayed}$ was the most accurate variable for LN staging. DTP PET/CT could provide improved diagnostic accuracy for the LN staging of NSCLC.