Pectin, a widely available and cost-effective polysaccharide, has garnered considerable attention in biomedical applications, particularly as a matrix for drug and gene delivery systems. Pectin possesses prominent properties such as biocompatibility, biodegradability, and low toxicity, which are desired features for delivery systems. Various pectin-based nanostructures have been applied to encapsulate therapeutic agents, drugs, and genetic materials with the potential of protecting them until selectively transfer to the objective tissue and sustainably release in controlled conditions. Pectin-based nanostructures have been widely used in oral drug delivery systems because of pectin's stability in the gastric and small intestine biological media. Moreover, pectin-based nanostructures have a high potential usage in liver cancer treatment due to the selective targeting of galactose groups of pectin to liver cancer cells' receptors. Despite applying pectin-coated nanocomposites as non-viral vectors of gene delivery, more clinical trials are required to develop such potential carriers in gene therapy. Pectin has unique biological features such as anticancer, antimicrobial, antioxidant, antidiabetic, and anti-cholesterol properties that synergistically enhance the efficiency of the drug/gene delivery system. This review presents an exhaustive investigation of the recent research on pectin-based nanostructures applied in drug/gene delivery systems and other biomedical applications, its advantages, challenges, and future perspectives.