Background Skip metastases are defined as lateral lymph node metastasis (LNM) without the involvement of central LNM in papillary thyroid cancer (PTC), and it is difficult to predict in clinical practice. Our study aimed to investigate the risk factors of skip metastasis and establish a nomogram for predicting the probability of skip metastasis in PTC patients. Patients and Methods A total of 378 consecutive PTC patients with clinically suspected LNM who underwent modified radical neck dissection (MRND) from March 2018 to July 2019 were enrolled in our hospital, Univariate and multivariate analyses were used to examine risk factors of skip metastasis, and a nomogram prediction model was established and internal validated. Results The incidence of skip metastasis was 11.9% (45/378). Primary tumor size ≦1cm(OR=2.703, 95%CI,1342-5.464; P =0.005 ), Age(OR=1.051, 95%CI, 1.017-1.805, P =0.005), Primary tumor location in the upper portion(OR=6.799, 95%CI, 2.710-17.060, P < 0.001)were found to be independent risk factors for skip metastasis in PTC patients. A nomogram based upon these predictors performed well. With an area under the curve (AUC) of 0.806 (95%CI,0.736-0.876) and the P value of the Hosmer-Lemeshow goodness of fit test was 0.66, Decision curve analysis revealed that nomogram was clinically useful. Conclusion Based on the risk factors of skip metastasis and established a high-performance nomogram, which can provide an individual risk assessment and guide treatment decisions for patients.