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A three-dimensional image reconstruction for fluorescence-enhanced frequency-domain photon migration (FDPM) measurements in turbid media is developed and investigated for three different simulated measurement types: 1) absolute emission measurement, or emission measurements of phase and amplitude attenuation made for a given incident point source of excitation light; 2) referenced emission measurements made relative to an excitation measurement conducted at a single reference point away from the incident source; and 3) referenced emission measurements made relative to the excitation measurement conducted at identical points of detection. The image reconstruction algorithm employs a gradient-based constrained truncated Newton (CONTN) method which implements a bounding parameter, which can be used to govern the level of contrast used to discriminate tissue volumes from heterogeneous background tissues. Reverse differentiation technique is used to calculate the gradients. Using simulated data with superimposed noise to achieve a signal-to-noise ratio of 55 and 35 dB to mimic experimental excitation and emission FDPM measurements, respectively, we show the robustness of emission measurements referenced to excitation light. We investigate the performance of algorithm CONTN using these measurement techniques and show that the absorption coefficients due to fluorophore are reconstructed by CONTN accurately and efficiently. Furthermore, we demonstrate the performance of the bounding parameter for rejection of background artifacts owing to background tissue heterogeneity.