3D Fluorescence Molecular Tomography (FMT) is an important pre-clinical tool for quantifying and characterizing molecular markers for different diseases. Herein, we demonstrate, for the first time, 3D K-Space FMT reconstructions using a large time-gated SPAD camera, SwissSPAD2 (SS2). The 3D reconstruction results are obtained using traditional and Deep Neural Network-based inverse solvers. Moreover, the 3D reconstruction performance with SS2 is benchmarked against that obtained with a gated-ICCD camera. The reconstruction results obtained using SS2 are in good agreement with those obtained from the gated-ICCD.