We have developed a fluorescence image reconstruction algorithm for three-dimensional whole-body small animal imaging. Our method uses non-contact fluorescent light measurement data on the tissue surface of the animal and reconstructs the three-dimensional unknown luorophore concentration inside the tissue. The image reconstruction technique em-ploys a light propagation model based on the equation of radiative transfer, which is solved on a structured Cartesian grid by a finite-difference method. A blocking-off approach takes the curved tissue surface geometry of the animal into account. Our proposed method has the advantage that fast numerical solvers for the equation of radiative transfer can be used.