Fullerene has been investigated for use in intratracheal instillation and inhalation. However, its use may be compromised due to the formation of reactive oxygen species (ROS) from a long-term stored water-soluble fullerene system, which will result in pulmonary injury. In this study, we investigated the ability of different concentrations of silk fibroin (SF) to scavenge hydroxyl radicals (OH˙) produced by a water-soluble fullerene system. In addition, we elaborated the mechanism of OH˙ formation and scavenging, the degradation of water-soluble fullerene (WSF), and the effects of OH˙ and WSF on the viability of endothelial cells (ECs). WSF was found to rapidly degrade when incubated with SF at 4 °C, which suggested that OH˙ and the deposition of WSF over 5 half-lives might be reduced by mixing WSF with SF. Moreover, it was observed that OH˙ and WSF could generate adverse effects on EC viability, and OH˙ produced by the WSF system on day 55 could be scavenged by SF. Overall, this study indicated that SF as an antioxidant was capable of scavenging OH˙ and accelerating the degradation of WSF, which provides further insight into the application of WSF in intratracheal instillation and inhalation.