Three naphthoquinone derivatives (plumbagin, juglone, and menadione) have been reported with antibacterial, antifungal, and antiviral properties and could potentially be used as anticancer agents because they can provoke apoptosis. However, they are also strong oxidants and cause cytotoxicity and even necrosis, so they are only limited to experimental chemotherapeutic use. In order to understand their physical chemical properties, we used both Fourier Transform Infrared Spectroscopy (FTIR) and Terahertz Time-Domain Spectroscopy (THz-TDS) to study their absorption spectra in wave number ranges of 400~4000 cm-1 and 6.6 ~ 92.4 cm-1. We also analyzed their characteristic absorption peaks, and assigned spectra peaks in IR range to their molecular structures. These data will be very useful in future studies of their pharmaceutical mechanisms.