Enzyme, which exists widely in organisms, has high specificity and high catalytic efficiency for its substrates. The absence, the reduced activity, or the overexpression of enzyme are closely related to the occurrence and development of diseases. Therefore, enzyme is often used as markers for disease detection and treatment. To detect enzyme activity and track drug release, aggregation-induced emission (AIE) bioprobes have been developed because of their excellent photostability and high signal-to-noise ratio (SNR). Among them, peptide-based AIE bioprobes with great biocompatibility and specificity are favored by an increasing number of researchers. Enzymatic hydrolysis of peptide can cause aggregation of AIE molecules and drug release. In this review, enzyme-responsive peptide-based AIE bioprobes used for biomedical application are summarized according to the three aggregation strategies triggered by various reaction between peptide and enzyme, including enzyme-triggered precipitate, enzyme-catalyzed coupling, and enzyme-instructed self-assembly. By giving some representative examples, we discuss how each aggregation strategy detects enzyme activity and treats the diseases under imaging guidance. Finally, we comment on the current problems and future prospects of enzyme-responsive peptide-based AIE bioprobes.