This paper builds on the context and recent progress on the control, reproducibility, and limitations of using graphene and graphene-related materials (GRMs) in biomedical applications. The review describes the human hazard assessment of GRMs in in vitro and in vivo studies, highlights the composition–structure–activity relationships that cause toxicity for these substances, and identifies the key parameters that determine the activation of their biological effects. GRMs are designed to offer the advantage of facilitating unique biomedical applications that impact different techniques in medicine, especially in neuroscience. Due to the increasing utilization of GRMs, there is a need to comprehensively assess the potential impact of these materials on human health. Various outcomes associated with GRMs, including biocompatibility, biodegradability, beneficial effects on cell proliferation, differentiation rates, apoptosis, necrosis, autophagy, oxidative stress, physical destruction, DNA damage, and inflammatory responses, have led to an increasing interest in these regenerative nanostructured materials. Considering the existence of graphene-related nanomaterials with different physicochemical properties, the materials are expected to exhibit unique modes of interactions with biomolecules, cells, and tissues depending on their size, chemical composition, and hydrophil-to-hydrophobe ratio. Understanding such interactions is crucial from two perspectives, namely, from the perspectives of their toxicity and biological uses. The main aim of this study is to assess and tune the diverse properties that must be considered when planning biomedical applications. These properties include flexibility, transparency, surface chemistry (hydrophil–hydrophobe ratio), thermoelectrical conductibility, loading and release capacity, and biocompatibility.