The objective of this study was the preparation of ionically crosslinked 6-mercaptopurine (6-MP) monohydrate microparticles through preparing polyelectrolyte complexes of drug and polymers. Polymers such as chitosan, casein, and carrageenan were used to prepare crosslinked microparticles, and sodium tripolyphosphate was used as crosslinker. Microparticles were characterized for their flow behavior, compressibility, percentage yield, micromeritic, and entrapment efficiency. Scanning electron microscopy was conducted to understand the surface morphology of the microparticles, and the result was correlated with the swelling index and percentage drug release. Mathematical modeling of drug release in order to determine the drug release kinetics was also determined to understand the mechanism involving the release of 6-mercaptopurine from the microparticles. The ionic crosslinked microparticles were in the range of 664 μm–798 μm particle size having good flow and compressibility properties with percentage yield were found to be from 77.5% to 87.5% in range. The entrapment efficiency for the formulations were found to be from 63.5% to 83.5%, with MCP-5 gave maximum entrapment efficiency of 83.5%. In vitro swelling and drug release studies were in accordance with the polymer properties following zero-order model with super-case transport II.