There is a renewed interest in the application of chitosan-based drug delivery systems over the last few years. In this study, the ionic gelation method was used to prepare chitosan-engaged tripolyphosphate ions, as the cross-linking molecule, (Chit-TPP) and concurrent loading of the biomolecules of the ethanolic extract of fennel, Foeniculum vulgare, seed (FEC@NBC). The samples were characterized by SEM, DLS, TGA, FTIR, XRD, GC-MS, and zeta potential, and their effects on the related hormonal and biochemical factors of the rats with polycystic ovarian syndrome (PCOS) were assessed. The estradiol valerate-induced PCOS in female rats was confirmed by vaginal smear test and subsequent histological screening. The PCOS-induced rats were treated by fennel seed extract (FSX), Chit-TPP, and FEC@NBC. The process of treatment was monitored by measuring the serum levels of testosterone, luteinizing hormone, follicle-stimulating hormone, insulin, glucose, high-density lipoprotein cholesterol, total cholesterol, and total triglyceride after 16 days of treatment and compared with healthy control and untreated PCOS-control groups. The FEC@NBC administration contributed to the remarkable hormonal, glucose, and lipid profile regulation in the rats with PCOS. The significance of FEC@NBC performance in dealing with PCOS complications compared to that of the only extract could be resulted from the effective targeted delivery and stability of phytomolecules when encapsulated in Chit-TPP.