Near-infrared fluorescence optical imaging has the unique opportunity of differentiating diseased lesions from normal lesions based upon environmentally indicated changes in the lifetime of a fluorescent imaging agent. In this paper, we demonstrate three-dimensional lifetime tomography using the gradient-based penalty modified barrier function with simple bounds truncated Newton with trust region method to reconstruct lifetime maps in a clinically relevant, single breast-shaped ( approximately 1081 cm(3)) phantom from point-frequency-domain photon migration measurements at 100 MHz. A reverse differentiation technique is used to calculate the gradients. This algorithm is desirable because the storage benefit from the use of the truncated Newton method and the reverse differentiation technique increase the speed. Two fluorescent contrast agents, indocyanine green and 3-3'-diethylthiatricarbocyanine iodide which differed in their fluorescence lifetimes by 0.62 ns, were used. Images of targets at a depth of 2.0 cm and target-to-background ratios (T:B) of 212:1 and 70:1 in fluoroscence absorption and 1:2.1 and 2.1:1 in lifetimes are successfully reconstructed. Our results show that image reconstruction is possible when there is (i) a longer lifetime in a target than the background and (ii) a shorter lifetime in a target than the background.