Regeneration of the intestinal epithelium after injury or during pathogenesis is a dynamic cellular process critical for host immunity. However, current epithelial injury models provide poor spatial control, complicating the study of precise cellular responses. Here we developed endoscopic femtosecond-laser surgery capable of generating acute tissue injury. A side-view probe provides a convenient access to the distal colon in the mouse in vivo and allows real-time intraoperative monitoring as well as pre- and post-surgery examinations via multiphoton imaging. The photo-induced damage showed a nonlinear dependence on laser intensity. At an optical power of 200 mW (2.5 nJ per pulse), scanning the beam focus over 300x300 µm² area in the colonic mucosa generated substantial vascular damages within 30 s. We confirmed the localized tissue damage and the physiologic regeneration of the disrupted epithelium by in situ barrier function assays, validating the animal model for epithelial regeneration following injury. The femtosecond endosurgery technique is applicable to various experimental models based on laser-induced perturbations.