Recently, antimicrobial activities of various carbon-based nanomaterials against specific pathogens have become one of the most significant research interests in this field. Carbon nanotubes (CNTs) are promising multidisciplinary nanostructures in biomedicine, drug delivery, genetic engineering, biosensors, and artificial implants. However, the biomedical administration of CNTs is dependent on their solubility, toxicity, and biocompatibility, as well as novel drug-delivery applications through optimization of the drug’s loading capacity, cellular absorption, and continuous release within the target cell. The usage of CNTs and Graphene materials as antimicrobial agents and nanocarriers for antibiotics delivery would possibly improve their bioavailability and facilitate better anti-infective therapy. However, it is worth mentioning that CNTs’ antimicrobial activity and toxicity are highly dependent on their preparation and synthesis method. Various types of research have confirmed that diameter, length, residual catalyst, metal content, surface coating, electronic structure, and dispersibility would affect CNTs’ toxicity toward bacteria and human cells. In this review article, a general study was performed on the antimicrobial properties of carbon-based nanomaterials, as well as their toxicity and applications in confronting different microorganisms. This study could be useful for researchers who are looking for new and effective drug delivery methods in the field of microbial resistance.