Naphthylimides play a pivotal role as aromatic heterocyclic compounds, serving as the foundational structures for numerous pharmacologically significant drugs. These drugs encompass antibacterial, antifungal, anticancer, antimalarial, antiviral, anti-inflammatory, antithrombotic, and antiprotozoal agents. The planar and heteroaromatic characteristics of naphthylimides grant them a strong ability to intercalate into DNA. This intercalation property renders naphthylimide derivatives highly valuable for various biological activities. The advantageous pharmacological activity and ease of synthesis associated with naphthylimides and their derivatives provide significant benefits in the design and development of new compounds within this class. Currently, only a few such molecules are undergoing preclinical and clinical evaluations. In this paper, we have compiled the literature on naphthylimides reported by researchers from 2006 to 2024. Our focus lies on exploring the pharmacological activities of their analogues from a drug development and discovery perspective, while examining their structure–activity relationship and mechanisms of action.