Background <p>Lymphoepithelial carcinoma (LEC) is a rare malignant tumor predominantly endemic to southern Asia and the Arctic regions, with only sporadic cases reported in Caucasian populations. As a subtype of poorly differentiated squamous cell carcinoma, LEC is difficult to diagnose preoperatively relying merely on clinical manifestations and imaging examinations, which easily leads to misdiagnosis.</p> Case presentation <p>We herein report a rare case of primary submandibular gland LEC in a Chinese patient. The patient was preoperatively misdiagnosed with pleomorphic adenoma of the left submandibular gland based on clinical and imaging features. However, postoperative pathological examination finally confirmed the diagnosis of malignant lymphoepithelial carcinoma rather than a benign salivary gland tumor.</p> Management and outcome <p>The patient received standardized surgical treatment and subsequent systematic follow-up. Individualized therapeutic strategies were formulated according to the definite pathological diagnosis to optimize patient prognosis.</p> Conclusion <p>This rare case reminds clinicians of the possibility of LEC in salivary gland space-occupying lesions. It is necessary to fully recognize the atypical clinical features of LEC and consider its malignant nature during surgical decision-making and postoperative treatment planning, so as to achieve accurate diagnosis and optimal individualized management for patients. </p>