BACKGROUND The pathogenesis of sporadic multiple meningiomas in the patients without history of neurofibromatosis type II remains unclear. We report whole exome sequencing (WES) of 2 metachronous multiple meningiomas of the same patient. CASE REPORT A 39-year-old female had a 5-month history of headache and her magnetic resonance imaging (MRI) revealed a significantly enhanced intracranial space-occupying pathology with dura tail sign and skull invasion. She had no history of neurofibromatosis type II or other tumors. Tumor resection achieved Simpson grade I and the pathological studies revealed an atypical meningioma. After surgery, she accepted focal external-beam radiation therapy. One year later, MRI showed a significantly enhanced intracranial space-occupying pathology near the primary site of the previous tumor. She had only a mild headache. Simpson grade I resection of the tumor was achieved. The pathological diagnosis was still an atypical meningioma. WES on both tumors identified 220 common somatic gene mutations and 43 different somatic gene mutations. Three deleterious mutated genes including QRICH2, KIF2C, and MUC16 were identified only in the first tumor, and 9 deleterious mutated genes including FCGBP, RPS6KA5, GOLGA6L2, IGHV3-66, RPTN, AGRN, USP6, CLTCL1, and PABPC3 were identified only in the second tumor. As shown by the identical result of 3 prediction tools, RPS6KA5 and AGRN were most likely to be related to the progress of multiple atypical meningiomas. CONCLUSIONS The metachronous meningiomas with same World Health Organization (WHO) grades in the same patient could have distinct genetic aberration patterns. The roles of RPS6KA5 and AGRN in the rapid progress of multiple atypical meningiomas need further studies.