Numerical performance of two gradient-based methods, a truncated-Newton method with trust region (TN) and a nonlinear conjugate gradient (NCG), is studied and compared for a given data set and conditions specific for the contrast enhanced optical tomography problem. Our results suggest that the relative performance of the two methods depends upon the error functions, specific to the problem to be solved. The TN outperforms the NCG when maps of fluorescence lifetime are reconstructed while both methods performed well when the absorption coefficient constitutes the parameter set that is to be recovered.