A series of indole and related benzo[g]indole compounds displaying potent activities against 5-lipoxygenase were selected to establish three-dimensional quantitative structure–activity relationships using comparative molecular field analysis and comparative molecular similarity indices analysis methods. A training set of 37 active compounds was used to develop the models, which were then valuated by a series of internal and external cross-validation techniques. A test set of seven compounds was used for the external validation. Models with greater than 70% predictive ability, as determined by external validation, and high internal validity (cross-validated q2 > 0.5) have been developed. The satisfactory comparative molecular field analysis model predicted a q2 value of 0.779 and an r2 value of 0.957 and revealed that electrostatic and steric properties play a significant role in potency. The best comparative molecular similarity indices analysis model, based on a combination of steric, hydrophobic, and H-bond donor effects, predicted a q2 value of 0.816 and an r2 value of 0.953. The models were graphically interpreted using comparative molecular field analysis and comparative molecular similarity indices analysis contour plots that provided insight into the structural requirements for increasing the activity of a compound. The results obtained from this study provide a solid basis for future rational design of more active 5-lipoxygenase inhibitors.