Since centuries, the rapid spread and cure of infectious diseases have been a major concern to the progress and survival of humans. These diseases are a global burden and the prominent cause for worldwide deaths and disabilities. Nanomedicine has emerged as the most excellent tool to eradicate and halt their spread. Various nanoformulations (NFs) using advanced nanotechnology are in demand. Recently, hydrogel and nanogel based drug delivery devices have posed new prospects to simulate the natural intelligence of various biological systems. Owing to their unique porous interpenetrating network design, hydrophobic drug incorporation and stimulus sensitivity hydrogels owe excellent potential as targeted drug delivery systems. The present review is an attempt to highlight the recent trends of hydrogel based drug delivery systems for the delivery of therapeutic agents and diagnostics for major infectious diseases including acquired immune deficiency syndrome (AIDS), malaria, tuberculosis, influenza and ebola. Future prospects and challenges are also described.