Discrepancies between radiological whole tumor size (RTS) and pathological whole tumor size (PTS) are sometimes observed. Unexpected pathological upsize may lead to insufficient margins during procedures like sub lobar resections. Therefore, this study aimed to investigate the current status of these discrepancies and identify factors resulting in pathological upsize in patients with early-stage non-small cell lung cancer (NSCLC). Data from a multicenter database of 3092 patients with clinical stage 0-IA NSCLC who underwent pulmonary resection were retrospectively analyzed. Differences between the RTS and PTS were evaluated using Pearson's correlation analysis and Bland-Altman plots. Unexpected pathological upsize was defined as an upsize of ≥1 cm when compared to the RTS, and the predictive factors of this upsize were identified based on multivariable analyses. The RTS and PTS showed a positive linear relationship (r = 0.659), and the RTS slightly overestimated the PTS. The Bland-Altman plot showed 131 of 3092 (5.2%) cases were over the upper 95% limits of agreement. In multivariable analyses, a maximum standardized uptake value (SUVmax) of the primary tumor on 18-fluoro-2-deoxyglucose positron emission tomography/computed tomography (odds ratio [OR], 1.070; 95% confidence interval [CI], 1.035−1.107; P < 0.001) and the adenocarcinoma histology (OR, 1.899; 95% CI, 1.071−3.369; P =0.049) were independent predictors of unexpected pathological upsize. More of the adenocarcinomas with pathological upsize were moderately or poorly differentiated, when compared to those without. The RTS tends to overestimate the PTS; however, care needs to be taken regarding unexpected pathological upsize, especially in adenocarcinomas with a high SUVmax.