Management of papillary thyroid microcarcinoma sized ≤5 mm identified on ultrasonography is controversial. In this study, we evaluated the clinical characteristics of papillary thyroid microcarcinoma sized ≤5 mm on ultrasonography in comparison to those >5 mm and sought to present rationales for optimal management in papillary thyroid microcarcinoma ≤5 mm. The medical records of 396 patients who underwent surgery for papillary thyroid carcinoma between 2009 and 2011 were retrospectively analyzed. The patients were grouped into A (≤5 mm, n = 132) or B (>5 mm, n = 264) and the clinicopathologic characteristics of the patients were reviewed and compared between the two groups. Tumor capsular invasion (45.5 vs. 59.8 %, p = 0.007) and cervical lymph node metastasis (18.2 vs. 29.2 %, p = 0.018) were more frequent in group B. Nonetheless, group A presented lymph node metastasis in 42.3 % of multifocal cases showing no difference to that of group B (41.5 %, p = 0.946) and also included five cases (3.8 %) of lateral neck metastasis. Multifocality was the only predictive factor for lymph node metastasis in group A (p < 0.001). Over half (55.3 %) of the patients of group A were diagnosed with papillary carcinoma in private clinics; however, only 5.5 % of these patients underwent assessment of lateral neck lymph nodes initially. In conclusion, higher risk of cervical lymph node metastasis should be considered in evaluation and surgical decision of papillary thyroid microcarcinoma ≤5 mm identified on ultrasonography with multifocality. Evaluation of the cervical lymph nodes including the lateral neck should not be overlooked when suspicious thyroid nodule suggesting malignancy sized ≤5 mm shows multifocal lesions.