Proteolytic enzymes expressed on the surface of tumor cells, and thus easily accessible to external interventions, represent useful targets for anticancer and antimetastatic therapies. In our study, we thoroughly evaluated matriptase, a trypsin-like transmembrane serine protease, as potential target for novel inhibitor-based tumor therapies. We applied time-domain near infrared fluorescence (NIRF) imaging to characterize expression and activity of matriptase in vivo in an orthotopic AsPC-1 pancreatic tumor model in nude mice. We show strong and tumor-specific binding of intravenously injected Cy5.5 labeled antimatriptase antibody (MT-Ab*Cy5.5) only to primary AsPC-1 tumors and their metastases over time within living mice, taking into account fluorescence intensities and fluorescence lifetimes of the applied probes. Specific binding of MT-Ab*Cy5.5 to tumor sites was confirmed by ex vivo NIRF imaging of tumor tissue, NIRF microscopy and by coregistration of the in vivo acquired NIRF intensity maps to anatomical structures visualized by flat-panel volume computed tomography (fpVCT) in living mice. Moreover, using an activatable synthetic substrate S*DY-681 we could clearly demonstrate that matriptase is proteolytically active in vitro as well as in vivo in tumor-bearing mice, and that application of synthetic active-site inhibitors having high affinity and selectivity toward matriptase can efficiently inhibit its proteolytic activity for at least 24 hr. We thus successfully applied NIRF imaging in combination with fpVCT to characterize matriptase as a promising molecular target for inhibitor-based cancer therapies.