The advancement of biomaterials utilization in biomedical and tissue regenerative applications has emerged progressively. Hydrogels are three-dimensional, hydrophilic polymeric networks that replicate the natural extracellular matrix (ECM), establishing a hydrated porous milieu that emulates biological functions such as proliferation and differentiation of cellular components. The application of biological macromolecules, particularly Heparin-based hydrogel, has garnered considerable interest owing to various intrinsic biological and mechanical properties. This comprehensive review paper is designed to elucidate the derivation of heparin and its purification method for biomedical uses. The article briefly outlines the diverse physiochemical and biological properties of heparin derivative-based hydrogels/scaffolds and emphasizes their significance as vehicles for growth factors, genes, and cells in complex biomedical and tissue engineering applications. This publication also summarizes the potential concerns associated with heparin-based derivatives, efforts to address these issues, and current clinical perspectives. This represents the inaugural instance of an extensive summarization of heparin-based hydrogels in biomedical applications, emphasizing pre-clinical and clinical investigations, which will further assist the scientific community in addressing the challenges associated with heparin-based hydrogels in biomedical contexts.