The unsurpassed properties in electrical conductivity, thermal conductivity, strength, and surface area-to-volume ratio allow for many potential applications of carbon nanomaterials in various fields. Recently, studies have characterized the potential of using carbon nanotubes (CNTs) as a biomaterial for biomedical applications and as a drug carrier via intravenous injection. However, most studies show that unmodified CNTs possess a high degree of toxicity and cause inflammation, mechanical obstruction from high organ retention, and other biocompatibility issues following in vivo delivery. In contrast, carbon nanocapsules (CNCs) have a lower aspect ratio compared with CNTs and have a higher dispersion rate. To investigate the possibility of using CNCs as an alternative to CNTs for drug delivery, heparin-conjugated CNCs (CNC-H) were studied in a mouse model of acute hindlimb thromboembolism. Our results showed that CNC-H not only displayed superior antithrombotic activity in vitro and in vivo but they also had the ability to extend the thrombus formation time far longer than an injection of heparin or CNCs alone. Therefore, the present study showed for the first time that functionalized CNCs can act as nanocarriers to deliver thrombolytic therapeutics.