In this study, conformer analysis of isomer structures of para-, meta- and ortho 4-methoxyphenyl piperazine molecules was performed using the Spartan 08 package program. The optimized geometrical parameters, energies for the highest occupied molecular orbital and the lowest unoccupied molecular orbitals, chemical reactivity descriptors, nonlinear optical properties, Mulliken population analysis, molecular electrostatic potential map, thermodynamic properties and UV–Vis spectral analysis of isomers of the N-(4-methoxyphenyl) piperazine molecule were predicted using the density functional theory (DFT) and TD-DFT/B3LYP/6-311++G(d,p) methods. The theoretical results obtained were compared with experimental results available in the literature so far, and these results were discussed for each isomer. Graphical abstract: [Figure not available: see fulltext.]