Mucinous borderline ovarian tumors (MBOTs) have a very low recurrence rate and a good prognosis, especially in the early stages, but some MBOTs occasionally recur with the progression to mucinous ovarian carcinomas (MOCs). Here, we present a case of MBOT that recurred as invasive MOC within 3 years. To examine the reason for the progression from MBOT to MOC, whole-exome sequencing of our case identified identical mutations and copy number alterations in KRAS, CDKN2A, and TP53 in both the MBOT and recurrent MOC. The recurrent MOC had a greater copy number alteration burden compared to the primary MBOT. These findings suggest that MBOT may have progressed to MOC via recurrence, wherein the increased burden of copy number alterations could be its key driver. It was also suggested that TP53 mutations already present in MBOT may contribute to the increased copy number alterations leading to MOC.