We performed a retrospective chart review of 245 patients with papillary thyroid microcarcinoma (PTMC) to define factors linked to central lymph node metastasis and thus prognosis. Univariate and multivariate analyses showed that being male (p < 0.001), age <45 years at diagnosis (p = 0.045), maximum tumor size > 5 mm (p = 0.030), multifocal tumor (p = 0.040) and tumor envelope invasion (p < 0.001) were all independent risk factors for central compartment lymph node metastasis. Unifocal lesions at the thyroid gland’s upper pole, middle and lower pole, had lymph node metastasis rates of 22.7%, 14.0% and 35.0%, respectively (p = 0.048). The rate of central lymph node metastasis was much higher when there was bilateral thyroid involvement than with multifocal unilateral lesions (58.6% vs 37.5%; p = 0.040). These results suggest that for patients at low risk of central lymph node metastasis, unilateral thyroid lobe and isthmus resection is sufficient. However, for patients at high risk of central lymph node metastasis, central lymph node dissection increases the likelihood of complete tumor excision.