Background The diagnostic accuracy of computed tomography (CT)-guided percutaneous core needle biopsy (CNB) for small (≤ 20 mm) ground-glass opacity (GGO) lesions has not been reported in detail. Objectives To evaluate factors that affect the diagnostic accuracy of CT-guided percutaneous CNB for small (≤ 20 mm) GGO pulmonary lesions. Methods From January 2014 to February 2018, 156 patients with a small (≤ 20 mm) GGO pulmonary lesion who underwent CT-guided CNB were enrolled in this study. Factors affecting diagnostic accuracy were evaluated by analyzing patient and lesion characteristics and technical factors. Significant factors were identified by multivariate logistic regression. Results The diagnostic accuracy of CT-guided percutaneous CNB was 90.4% for small (≤ 20 mm) GGO pulmonary lesions. The diagnostic accuracy was higher for larger lesions (72.5% for lesions ≤ 10 mm, 96.6% for lesions between 11 and 20 mm [P < 0.001]). The diagnostic accuracy of CT-guided percutaneous CNB was 74.5% for lesions with > 90% GGO components and 97.2% for lesions with 50–90% GGO components (P < 0.001). In multivariate analysis, the significant factors influencing diagnostic accuracy were lesion size (P = 0.022; odds ratio [OR] for a lesion between 11 and 20 mm in size was approximately 5 times higher than that for a lesion ≤ 10 mm; 95% confidence interval [CI], 1.3 to 18.5), and GGO component (P = 0.015; OR for a lesion with 50–90% GGO components was approximately 6 times higher than that for a lesion with > 90% GGO components; 95% CI: 1.4 to 25.7). Conclusions Lesion size and GGO component are factors affecting diagnostic accuracy. The diagnostic accuracy was higher for larger lesions and lesions with 50–90% GGO components.