Metal nanoclusters (NCs), comprising tens to hundreds of metal atoms, are condensed matter with concrete molecular structures and discrete energy levels. Compared to metal atoms and nanoparticles, metal NCs exhibit unique physicochemical properties, especially fascinating electrocatalytic activities. This review focuses on recent progress in the precise synthesis of metal NCs and their applications in electrochemical analysis of various disease biomarkers. First, we provide a brief overview of current nanotechnology-enabled electrochemical biosensors. Subsequently, we highlight the precise synthesis of metal NCs protected by various ligands such as peptides, proteins and nucleic acids. Next, we summarize the design and construction of electrochemical biosensors that utilize metal NCs as electrode materials to detect electrochemically active and inactive disease-associated biomarkers, including small biomolecules (glucose, reactive oxygen species, cholesterol, neurotransmitters and amino acids) and biomacromolecules (proteins, enzymes, and nucleic acids). Due to unique electrocatalytic properties, high specific surface areas, and atomically modulated structures, metal NCs promote electron exchange or act as a redox medium in these electrochemical sensing platforms. Finally, we conclude with present challenges and propose future research directions, with the aim to enhance the specificity, sensitivity, and durability of customized metal NC-based electrochemical biosensors for precise disease diagnostics.