Echinochrome A, a natural naphthoquinone pigment found in sea urchins, is increasingly being investigated for its nutritional and therapeutic value associated with antioxidant, anticancer, antiviral, antidiabetic, and cardioprotective activities. Although several studies have demonstrated the biological effects and therapeutic potential of echinochrome A, little is known regarding its biopharmaceutical behaviors. Here, we aimed to investigate the physicochemical properties and metabolic profiles of echinochrome A and establish a physiologically-based pharmacokinetic (PBPK) model as a useful tool to support its clinical applications. We found that the lipophilicity, color variability, ultraviolet/visible spectrometry, and stability of echinochrome A were markedly affected by pH conditions. Moreover, metabolic and pharmacokinetic profiling studies demonstrated that echinochrome A is eliminated primarily by hepatic metabolism and that four possible metabolites, i.e., two glucuronidated and two methylated conjugates, are formed in rat and human liver preparations. A whole-body PBPK model incorporating the newly identified hepatic phase II metabolic process was constructed and optimized with respect to chemical-specific parameters. Furthermore, model simulations suggested that echinochrome A could exhibit linear disposition profiles without systemic and local tissue accumulation in clinical settings. Our proposed PBPK model of echinochrome A could be a valuable tool for predicting drug interactions in previously unexplored scenarios and for optimizing dosage regimens and drug formulations.