Controlled release of drugs is an important strategy to diminish the drug dose and adverse side effects. Aqueous mixtures of polysaccharides and proteins are usually unstable above a certain biopolymer concentration and phase separation occurs either because of repulsive (segregative) or attractive (associative) interactions. Herein, pectin/casein microcapsules were prepared by complex coacervation aiming at prolonged drug release. The morphological characteristics, particle size, distribution, and release kinetics of microcapsules were studied using as a model the hydrophilic drug acetaminophen. It was detected that complexation of pectin/casein particles occurs at pH values lower than 6, resulting in the formation of spherical particles after spray drying. Microcapsules had a mean diameter of 3.138 and 4.929 μm without drug, and of 4.680 and 5.182 μm with drug using USP and 8003 pectin, respectively. The in vitro release of acetaminophen from microcapsules was slow and the drug release mechanism was controlled by diffusion following first-order kinetics. There was greater release of acetaminophen in simulated gastric fluid than simulated intestinal fluid conditions. Concluding, the polymeric system present herein seemed to be appropriate for a prolonged release of acetaminophen throughout the gastrointestinal tract. Nevertheless, it is likely that it is a promising pectin/casein complex for lipossoluble drugs, which merits further investigation.