Recent next‐generation sequencing (NGS) studies have shown that synchronous endometrial and ovarian cancers (SEOCs) are often derived from the same clone. However, the clonal relationship in Lynch syndrome remains unclear. A 45‐year‐old woman was diagnosed with grade 2 endometrial endometrioid carcinoma and an ovarian yolk sac tumor with clear cell carcinoma. Genetic testing revealed different MLH1 variants in the endometrial and ovarian cancers, and peripheral blood analysis identified an exon 5 deletion in MLH1 , confirming Lynch syndrome. The somatic variants in the tumors were distinct. A review of the literature found six cases of SEOC in Lynch syndrome with NGS‐based clonal analysis, four of which (67%) showed independent cancers with different somatic profiles. These findings suggest that, unlike sporadic SEOC, synchronous cancers in Lynch syndrome are more likely to arise from separate clones.