Bufotenine (5-hydroxy-N,N-dimethyltryptamine) is a natural tryptamine derivative with hallucinogenic activity. In this paper, we present novel chemical and molecular conformational analyses of bufotenine based on an experimental and theoretical approach integrating surface-enhanced Raman scattering (SERS) and density functional theory (DFT). For the first time, low concentrations of bufotenine in acetonitrile solutions were analyzed by SERS using two types of silver nanoparticle substrates synthesized via one- or two-step reduction processes. The vibrational characteristics of this molecule were verified by molecular dynamics simulations of Raman bands based on DFT. Here we demonstrate the potential of this integrated approach for the identification of bufotenine, a prominent hallucinogenic agent, establishing an innovative rapid and accurate sensing and characterization method of the identification of controlled substances at trace amounts.