Fluorescent nanomaterials have exhibited promising applications in biomedical and tissue engineering fields. To improve the properties and expand bioapplications of fluorescent nanomaterials, various functionalization and biomodification strategies have been utilized to engineer the structure and function of fluorescent nanomaterials. Due to their high biocompatibility, satisfied bioactivity, unique biomimetic function, easy structural tailoring, and controlled self‐assembly ability, supramolecular peptides are widely used as versatile modification agents and nanoscale building blocks for engineering fluorescent nanomaterials. In this work, recent advance in the synthesis, structure, function, and biomedical applications of peptide‐engineered fluorescent nanomaterials is presented. Firstly, the types of different fluorescent nanomaterials are introduced. Then, potential strategies for the preparation of peptide‐engineered fluorescent nanomaterials via templated synthesis, bioinspired conjugation, and peptide assembly‐assisted synthesis are discussed. After that, the unique structure and functions through the peptide conjugation with fluorescent nanomaterials are demonstrated. Finally, the biomedical applications of peptide‐engineered fluorescent nanomaterials in bioimaging, disease diagnostics and therapy, drug delivery, tissue engineering, antimicrobial test, and biosensing are presented and discussed in detail. It is helpful for readers to understand the peptide‐based conjugation and bioinspired synthesis of fluorescent nanomaterials, and to design and synthesize novel hybrid bionanomaterials with special structures and improved functions for advanced applications.