A nanodiamond (ND) is a promising material for drug delivery applications owing to its relatively low cost, amenability to large-scale synthesis, unique structure, and low toxicity. However, synthesizing drug-loaded ND conjugates with uniform and tunable sizes, high loading capacity, efficacy in drug delivery, and versatility in terms of surface functionalization has been challenging. Here, we show that perfluorooctanoic acid-functionalized NDs spontaneously transform into well-dispersed and biocompatible supraparticle (SP) nanoclusters. We demonstrate that the synthesized ND-based SPs (ND-SPs) exhibit high penetration through the cell membrane and are therefore superior as drug carriers for conventional nanomedicines such as polyethylene glycol and phospholipid-based nanocapsules and simple drug-loaded ND conjugates. We confirm the efficacy of ND-SPs in the eradication of cancer cells in vitro and in vivo. Our results demonstrate that the synthesized ND-SPs are useful for targeted drug delivery in a variety of biological applications.