Because lymph node (LN) metastasis has been proven to be a predictor for locoregional recurrence (LRR) in papillary thyroid microcarcinoma (PTMC), better knowledge about the predictors for LN metastasis in PTMC is required. We retrospectively reviewed 5656 PTMC patients who underwent total thyroidectomy and central neck dissection and/or lateral neck dissection between January 1997 and June 2015. Male gender (adjusted odds ratio [OR] 2.332), conventional variant (adjusted OR 4.266), tumor size >0.5 cm (adjusted OR 1.753), multiplicity (adjusted OR 1.168), bilaterality (adjusted OR 1.177), and extrathyroidal extension (ETE) (adjusted OR 1.448) were independent predictors for high prevalence of central LN metastasis (CLNM), whereas per 10-year age increment (adjusted OR 0.760) and chronic lymphocytic thyroiditis (adjusted OR 0.791) were independent predictors for low prevalence of CLNM. In addition, male gender (adjusted OR 1.489), tumor size >0.5 cm (adjusted OR 1.295), multiplicity (adjusted OR 1.801), ETE (adjusted OR 1.659), and CLNM (adjusted OR 4.359) were independent predictors for high prevalence of lateral LN metastasis (LLNM), whereas per 10-year age increment (adjusted OR 0.838) was an independent predictor for low prevalence of LLNM. There was a statistically significant difference in LRR with regard to nodal stage (p < 0.001). Meticulous perioperative evaluation of LN metastasis is required for PTMC patients with the above predictors.