The low effectiveness of various brain cancer treatment methods is due to a number of significant challenges. Most of them are unable to penetrate the blood-brain barrier (BBB) when drugs are administered systemically through the bloodstream. Nanoscale particles play a special role among materials capable of binding drug molecules and successfully crossing the BBB. Biopolymeric nanoparticles (NPs) demonstrate excellent biocompatibility and have the remarkable ability to modify the environment surrounding tumor cells, thereby potentially improving cellular uptake of delivery agents. In our research, nanoscale polyelectrolyte complexes (PECs) ranging in size from 56 to 209 nm were synthesized by ionic interaction of the oppositely charged polysaccharides pectin and chitosan. The structural characteristics of these complexes were carefully characterized by infrared (FTIR) and Raman spectroscopy. The immobilization efficiency of antitumor drugs was comprehensively evaluated using UV spectrophotometry. The cytotoxicity of the NPs was evaluated in the U87-MG cell line. The preliminary data indicate a significant decrease in the metabolic activity of these tumor cells. Important details on the interaction of the NPs with an endothelial layer structurally similar to the BBB were obtained by simulating the BBB using a model based on human blood vessels. Our studies allowed us to establish a significant correlation between the kinetic parameters of drug immobilization and the ratio of biopolymer concentrations in the initial compositions, which provides valuable information for future optimization of drug delivery system design.