Background: Management of N0 neck in patients with head and neck squamous cell carcinoma (HNSCC) remains a subject of continued debate. Prognostic biomarkers might provide useful information for treatment selection and adjustment. Objective: To evaluate the prognostic relevance of VEGF-A and Ki-67 expression to types of neck management. Methods: This prospective study included 140 patients with HNSCC. Tumor expression of VEGF-A and Ki-67 was measured by immunohistochemistry. Based on tumor size and site criteria, 88 patients with N0 neck were categorized as high, intermediate and low risk of subclinical neck diseases and accordingly treated by elective neck dissection (END), irradiation (ENI) and observation. Adjuvant treatment was given to tumor with close or positive margins. A multivariate Cox regression model was used to identify prognostic factors. Impact of biomarker expression, treatment type and risk category on disease-specific survival (DSS) in the setting of N0 neck were evaluated by Kaplan-Meier survival and adjusted hazard ratio (HR). Results: Coexpression of VEGF-A and Ki-67 (HR = 2.351, p = 0.021) and positive node (HR = 2.301, p = 0.009) were independent prognostic factors for HNSCC. In the setting of N0 neck, marker coexpression has an HR of 4.97 (p = 0.004) independent of treatment modalities (p = 0.069) and risk categories (p = 0.971). Alternatively, neither marker expression was predictive of a better treatment outcome for END compared to ENI, as suggested by the odds of patients being survived 15.4 times greater (p = 0.01) and the 5-year DSS rates of 85.1% versus 44.7% (p = 0.008). Conclusion: Coexpression of VEGF-A and Ki-67 is a suggestion of tumor microinvasiveness in addition to risk of lymph node metastasis and may indicate the need of adjuvant treatment despite negative tumor margins. Neither marker expression serves an indicator for the selection of END over ENI in neck management.