High-throughput virtual screening (HTVS) has been increasingly applied as an effective approach to find candidate materials for energy applications. We performed a HTVS study, which is powered by: (i) automated virtual screening library generation, (ii) automated search on a readily purchasable chemical space of quinone-based compounds, and (iii) computed physicochemical descriptors for the prediction of key battery-related features of compounds, including the reduction potential, gravimetric energy density, gravimetric charge capacity, and molecular stability. From the initial virtual library of approximately 450k molecules, a total of 326 compounds have been identified as commercially available. Among them, 289 of the molecules are predicted to be stable for the sodiation reactions that take place at the sodium-ion battery cathodes. To study the behaviour of molecules over time at room temperature, we performed molecular dynamics simulations on a group of sodiated product molecules, which was narrowed down to 21 quinones after scrutinizing the key battery performance indicators. As a result, 17 compounds are suggested for validation as candidate cathode materials in sodium-ion batteries.