Extracellular vesicles (EVs), which are secreted by almost all living cells and play crucial roles in various physiological processes, have attracted increasing research interest. Numerous protocols for EV isolation, such as ultracentrifugation and polymer precipitation, have been developed; however, each conventional method has inherent strengths and limitations, particularly regarding purity, yield, and bias toward specific EV subpopulations. Herein, we present an EV isolation method, hydrogel adsorption separation (HAS), which uses a hydrogel scaffold for the selective and high-purity isolation of EVs from diverse biofluids. HAS leverages the affinity between membrane vesicles and palmitoyl groups on the hydrogel surface, enabling the isolation of less-biased EV subpopulations. EVs isolated using the HAS method were compatible with downstream analyses, including proteomics and flow cytometry, demonstrating their suitability for both basic and applied research. This approach is a practical and versatile tool for advancing the EV-based research and applications.