A method and system for non-contact fluorescent optical tomography using patterned illumination is disclosed. The method comprises illuminating a surface of a medium with light from at least one excitation light source to project at least two patterns. Each pattern comprises at least one motif, wherein the medium comprises at least one fluorescent target. The method further comprises for each pattern, measuring excitation light reflected from the medium to generate an excitation data set. In addition, the method comprises, for each pattern, measuring fluorescence emitted from the at least one fluorescent target to generate a fluorescence data set. The method also comprises generating a 3D image of the at least one fluorescent target in the medium by applying iterative algorithm. The iterative algorithm minimizes the difference between a predicted data set based on a mathematical model, and each excitation data set and each fluorescence data set.