Self‐assembling peptide‐based nanoprobes have attracted increasing research interest in recent years because of their inherent advantages, such as good biosafety, flexible designability, ease of synthesis, and degradability. Being precisely regulated by a delicate molecular design, the self‐assembly/disassembly behavior of the peptide‐based nanoprobes to external stimuli results in signal turn‐on/off properties, which can therefore be applied for disease theranostics and disease‐related molecular detection, including cancer, bacterial infection, cell imaging, and enzymes. This review summarizes the recent advancements of self‐assembled peptide‐based nanoprobes for disease diagnosis and molecular imaging. Moreover, the challenges and strategies of self‐assembled peptide‐based nanoprobes for clinic transformation and practical applications are briefly discussed.