Malignant ovarian germ cell tumors (MOGCT) are rare and often aggressive cancers that predominantly affect young women. Fortunately, combined surgery and chemotherapy results in high cure rates. In this review, we will consider some of the many controversies and poorly understood areas in the management of MOGCT that have arisen largely because of the lack of randomized trial data. This paucity of strong evidence is unsurprising, given the rarity of MOGCT and their multiple subtypes which differ biologically and in their clinical behavior. We will explore what is known about the biology and prognostic factors, and how the disease differs from its much more common and robust evidence-based male testicular counterpart. The type and extent of surgery, the value of surveillance in early-stage disease, and the role of neoadjuvant chemotherapy in advanced cases remain uncertain. In addition, optimizing outcomes in relapsed disease following initial chemotherapy is a key area for future development, as survival in this situation is worse than that in patients with testicular germ cell tumors. Fertility preservation remains of central importance, but the best way to achieve it remains debated. Finally, the type and duration of surveillance after treatment remain unclear. These and other controversies are discussed below.