To evaluate the effectiveness and complications of core-needle biopsy (CNB) compared to fine-needle aspiration (FNA) for diagnosing thyroid malignancy. The Ovid-MEDLINE and EMBASE databases were searched for studies using CNB for diagnosing thyroid malignancy. A meta-analysis was performed to evaluate the diagnostic accuracy, the incidence of non-diagnostic, inconclusive results, and the complications of CNB and FNA. To overcome the heterogeneity, additional analyses based on three, homogeneous inclusion criteria were performed and subgroup analyses were performed. Twenty eligible studies of 4580 patients (4746 nodules) were included. Both CNB and FNA demonstrated a high sensitivity (91 %, 74 %, respectively; p = .053) and specificity (99 %, 100 %, respectively; p = .914). The area under the curve was larger in CNB (0.99) than in FNA (0.94). CNB demonstrated a significantly lower pooled proportion of non-diagnostic (5.5 %; p < .001) and inconclusive results (8.0 %; p < .001) than FNA (22.6 %, 40.2 %, respectively). The complications rate of FNA (0.0 %) was lower than that of CNB (0.01 %), although not significantly (p = .948). This meta-analysis showed variable heterogeneities, i.e., no heterogeneity to considerable heterogeneity. Additional meta-analyses based on three, homogeneous inclusion criteria demonstrated that heterogeneities were reduced, and the results are in agreement with those of all of the included studies. Subgroup analyses have explained the cause of heterogeneity across studies. Both CNB and FNA may be acceptable diagnostic tools for diagnosing thyroid malignancy. CNB may be a complementary diagnostic tool in nodules with initially non-diagnostic and indeterminate results on previous FNA.