Mucinous ovarian carcinoma is a rare epithelial ovarian cancer with distinct biological features and limited sensitivity to standard chemotherapy, making molecularly guided treatment strategies increasingly relevant. We report the case of a 44-year-old woman who developed pulmonary metastases three years after the diagnosis of a mucinous borderline ovarian tumour. Immunohistochemistry and molecular profiling confirmed the ovarian origin of the metastatic lesions. After disease progression following six cycles of platinum-based chemotherapy, molecular analysis revealed a BRAF V600E mutation, and treatment with dabrafenib and trametinib was initiated, resulting in early disease progression. Due to HER2 expression (immunohistochemistry 2+, fluorescence in situ hybridisation negative) and the absence of alternative therapeutic options, trastuzumab deruxtecan was subsequently administered, achieving durable disease control for more than 14 months. This case underscores the importance of comprehensive histopathologic and molecular evaluation to confirm tumour origin in atypical metastatic presentations and to guide individualised treatment in rare ovarian tumours. It also highlights the potential clinical benefit of biomarker-driven therapies, including HER2-targeted antibody-drug conjugates, beyond conventional chemotherapy.