Background The Milan System for Reporting Salivary Gland Cytopathology (Milan System) has previously shown its diagnostic utility by categorizing the seven cytology findings in salivary gland lesions. However, there has been lack of study about the risk of high‐grade malignancy in the cytology diagnosis based on the Milan System. Thus, we tried to identify the diagnostic ability of the Milan System for high‐grade malignancy and to suggest an improved diagnostic approach for preoperative estimation of high‐grade malignancy using the Milan System. Methods A total of 413 patients with parotid gland tumors, who had undergone surgical resection from 2011 to 2015 were included in the present study retrospectively. Cytopathology was reclassified according to the Milan System by two independent reviewers. The outcomes were risk of malignancy and risk of high‐grade malignancy. The diagnostic performance of the Milan System category [Malignant] for detecting high‐grade malignancy was calculated. Results The risk of malignancy was 83.3% and 100% in the Milan System categories [Suspicious for Malignancy] and [Malignant], respectively. Meanwhile, the risk of high‐grade malignancy was 16.7% and 55.9% in these two categories. Disease‐free survival of patients with high‐grade malignancy was significantly worse than those with low‐ and intermediate‐grade malignancy. Union combining the Milan System category [Malignant] with the presence of nodal metastasis suggested high‐grade malignancy with an acceptable diagnostic sensitivity (0.889‐0.963) and negative predictive value (0.900‐0.966). Conclusions The Milan System category [Malignant] with the presence of nodal metastasis suggested parotid gland tumors as high‐grade malignancy in a pretreatment setting.