Thrombosis, the formation of blood clots within a blood vessel, can lead to severe complications including pulmonary embolism, cardiac arrest, and stroke. The most widely administered class of anticoagulants is heparin‐based anticoagulants such as unfractionated heparin (UFH), low‐molecular weight heparins (LMWHs), and fondaparinux. Protamine is the only FDA approved heparin antidote. Protamine has limited efficacy neutralizing LMWHs and no reversal activity against fondaparinux. The use of protamine can lead to complications, including excessive bleeding, hypotension and hypersensitivity, and has narrow therapeutic window. In this work, we present a new concept in the design of a universal heparin antidote: switchable protonation of cationic ligands. A library of macromolecular polyanion inhibitors (MPIs) was synthesized and screened to identify molecules that can neutralize all heparins with high selectivity and reduced toxicity. MPIs were developed by assembling cationic binding groups possessing switchable protonation states onto a polymer scaffold. By strategically selecting the identity and modulating the density of cationic binding groups on the polymer scaffold, a superior universal heparin reversal agent was developed with improved heparin‐binding activity and increased hemocompatibility profiles leading to minimal effect on hemostasis. The activity of this heparin antidote was demonstrated using in vitro and in vivo studies.This article is protected by copyright. All rights reserved