Histatin-5 (Hst-5) is a human salivary peptide with antibacterial and antifungal activities. Thorough characterization and reliable quantification of Hst-5 and its degradation products are essential for understanding the Hst-5 degradation pathway. Due to the highly basic and strong cationic nature of the Hst-5 peptide, the quantitative analysis of Hst-5 and its degradation forms by online mass spectrometry remains challenging. Here, we adopt a recently developed electrokinetically pumped sheath liquid capillary electrophoresis - mass spectrometry (CE-MS) coupling technology, and successfully apply it for the analysis of Hst-5 and its degradation products. Our CE-MS method is demonstrated to be robust and quantitative. This novel analytical platform is reproducible and free of sample carryover. The efficacy of this method is demonstrated with a kinetic study of Hst-5 degradation by Sap9, a secreted aspartic peptidase. Our work demonstrates the potential of online CE-MS as a powerful approach for characterizing highly basic peptides.