Punicic acid has been shown to exhibit anti-cardiovascular, anti-osteoporosis, antidiabetic, anti-inflammatory, and anticancer activities in both in vitro and in vivo studies. In this study, the inclusion complex of fatty acids (FA) from pomegranate seed oil, containing more than 70% punicic acid, with β-cyclodextrin (bCD) was comprehensively investigated. The inclusion complex (FA_bCD) was prepared by the co-precipitation method under optimal conditions: a bCD concentration of 10 mM and a molar ratio of bCD to FA of 2:1. The characteristics of the complex were studied using IR, XRD, TGA, SEM, and 1H NMR spectrometry. The geometries of the inclusion complex of punicic acid with bCD (Pu_bCD) were explored using DFT calculations (B3LYP/6-31G) with semi-empirical dispersion correction. The FA_bCD complex was formed in a 1:1 stoichiometry, and a stability constant of 1365 M−1 at 40 °C was determined. The antioxidant activity and ability to inhibit MCF-7 cell growth of the inclusion complex and fatty acid were compared, providing a theoretical basis for the further development and utilization of FA_bCD complexes. © 2025 Elsevier B.V., All rights reserved.