Unlike its other halogen atom siblings, chlorination of a bioactive compound can change its physiological characteristics, improve its pharmacological profile, and function as a point of diversification through cross‐coupling reactions. As a result, it has been a crucial strategy for drug discovery and development. However, functional groups such as amines, amides, hydroxy groups, or carboxylic acids trap the Cl+, severely limiting the reactivity and making direct chlorination far too difficult to be practical. Herein, we introduce a nucleophilic sulfonohydrazide catalyst for late‐stage halogenation of peptides and drugs. This direct, mild and metal‐free protocol shows high functional‐group tolerance and is compatible with a range of structurally diverse peptides, drugs and aromatic compounds. Furthermore, DFT studies indicate that the reaction most likely proceeds via a cationic transition state. The gram‐scale synthesis, high stability and efficiency of the catalyst provide a facile route for late‐stage functionalization and intermediates for further derivatization.