Radiation-induced lung damage is a major limiting factor to escalate dose in thoracic irradiation to achieve better tumor control while maintaining good quality of life for patients. We are investigating the role of mesenchymal stem cells (MSCs) transplantation for protection and recovery of radiation-induced lung injury using a rat model. In this work, we evaluate the use of fluorescence endomicroscopy to image inside the lungs at the cellular level in order to assess the extent of lung damage and evaluate the efficacy of MSCs treatment. Sprague Dawley rats were treated with 16 Gy hemithorax irradiation followed by MSCs injection once a week for six weeks via different administration routes: intravenous (IV), endotracheal (ET) or intraperitoneal (IP), control with sham radiation (Ctrl), and radiation treatment alone (RT). Twenty-two weeks post-radiation, the rats were imaged with endomicroscopy. The fiber optic probe was inserted into the lungs through a tracheotomy and images were acquired in the green channel. We assessed fibrosis with autofluorescence imaging and we used a blood vessel fluorescent marker (FITC-Dextran) to assess vasculature damage. In order to enhance the autofluorescent structures, we generated maximum intensity projection (MIP) images and used normalized cross-correlation (NCC) to compare the different conditions. To describe the vascular structures, we used texture analysis on 100 randomly selected frames averaged 10 times and computed percent differences. MIP images computed from autofluorescence videos showed bright structures in the lungs of RT rats but not in Ctrl. NCC analysis of fibrotic damage estimated low correlation of 0.03 for Ctrl to RT and 0.08 for Ctrl to IP. In contrast, we found a higher correlation of 0.15 and 0.27 for Ctrl to IV and ET, respectively. Regarding vasculature, we observed a reduction in flow as well as disrupted architecture and permeability of the vessels in RT compared to Ctrl with an intermediate phenotype in ET. This was confirmed by two texture analysis metrics: coarseness (C) that shows local uniformity and busyness (B), which describes the spatial rate of change in intensity. The largest difference was found for Ctrl to RT (C = -58 ± 5 %, B = 54 ± 4 %) and a similar trend in case of ET to RT (C = - 47 ± 2 %, B = 23 ± 1 %). In contrast, we found smaller differences between Ctrl to ET (C = -38 ± 6 %, B = 18 ± 5 %). We demonstrated the potential of endomicroscopy as a novel imaging method for assessing lung fibrosis and vasculature damage status post-radiation therapy. We were able to observe a large difference between RT and Ctrl with an intermediate response for ET. This highlights the potential of MSCs treatment and suggests that ET MSCs administration is the preferable delivery method as it shows less damage compared to IV or IP.