A comprehensive study of release kinetics of a hydrophilic drug from bio-aerogels based on pectin was performed. Pectin aerogels were made by polymer dissolution, gelation (in some cases this step was omitted), solvent exchange and drying with supercritical CO. Theophylline was loaded and its release was studied in the simulated gastric fluid during 1 h followed by the release in the simulated intestinal fluid. Pectin concentration, initial solution pH and concentration of calcium were varied to tune the properties of aerogel. The kinetics of theophylline release was monitored and correlated with aerogel density, specific surface area, and aerogel swelling and erosion. Various kinetic models were tested to identify the main physical mechanisms governing the release.