Cancer is responsible for high mortality rates worldwide, representing a serious health problem. In this sense, melanoma corresponds to the most aggressive type of skin cancer, being the cause of the highest death rates. Therapeutic strategies for the treatment of melanoma remain limited, with problems associated with toxicity, serious side effects, and mechanisms of resistance. The potential of natural products for the prevention and treatment of melanoma has been reported in different studies. Among these compounds, naphthoquinones (1,2-naphthoquinones and 1,4-naphthoquinones) stand out for their diverse pharmacological properties, including their antitumor activity. Thus, this review covers different studies found in the literature on the application of natural naphthoquinones targeting melanoma, providing information regarding the mechanisms of action investigated for these compounds. Finally, we believe that this review provides a comprehensive basis for the use of natural naphthoquinones against melanoma and that it may contribute to the discovery of promising compounds, specifically naphthoquinones, aimed at the treatment of this cancer.