Microcystic stromal tumor of the ovary (MSTO) is an exceedingly rare, unusual, and recently described entity with unique genetic alterations that assist in its diagnosis. We describe the case of a 50-year-old woman who presented with a complex right ovarian mass. A hysterectomy with bilateral salpingo-oophorectomy was performed and revealed an ovarian mass consistent with MSTO by histomorphology and immunohistochemical studies. Tumor cells were immunohistochemically reactive for vimentin, CD10, β-catenin, and Wilms tumor 1. In addition, we detected a missense mutation c.101 G>A, p.G34E in exon 3 of the β-catenin (CTNNB1) gene, which leads to an amino acid substitution of glycine at codon 34 by glutamic acid. The utility of genetic testing of this tumor and additional reporting of alterations detected is needed to verify pathogenicity of variants detected, as well as their potential roles with prognosis, behavior, and therapeutic targets. The overall clinical course of MSTO appears to be nonaggressive, although the number of reported cases are limited thus far.