The incidence of synchronous multiple primary lung cancer (SMPLC) has been increased in recent years. Because of a variance in clinical management and outcome, it is important to distinguish SMPLC from a primary tumor with intrapulmonary metastases. Here, we reported a diagnosis and treatment procedure regarding a case of a 58-year-old woman who presented with synchronous multiple tumor lesions in separate lungs. Using a next generation sequencing technology, a discordant EGFR gene profile from the separate lungs was revealed for this patient. After standard treatment procedures, the therapeutic effects were evaluated by response evaluation criteria in solid tumors (RECIST). This case shows an essential role in the combination of molecular features, together with pathological analysis, during the management of SMPLC, but challenges still required considering during dealing the cases of SMPLC.