Photodynamic inactivation (PDI) is a promising alternative for the treatment of infectious diseases, and the combination of indocyanine green (ICG) and extracorporeal infrared light has shown optimistic results against pneumonia in vitro and in vivo. However, the pharmacokinetics and the possible side effects of the pulmonary delivery via nebulization have not been fully investigated. This study assessed the distribution of the photosensitizer within the lungs and to other organs of mice, and monitored the fluorescence of ICG in the thorax in the presence and absence of the activating light. The excitation wavelength was 780 nm and detection focused on the emission between 795 and 890 nm. Experiments demonstrated that the amount of fluorescence detected from outside the body was significantly higher after the nebulization of ICG, and reduced after the illumination, allowing for the monitoring of the PDI in real time. The fluorescence remained detectable in the mice for at least 24 hours, and was present in the lungs, stomach, liver, small and large intestines, bladder, spleen and heart after this time.