Human fatty acid synthase (hFAS) is a megasynthase whose main function is de novo biosynthesis of saturated fatty acids. Interest has been drawn to this enzyme beyond its physiological role due to the association between high levels of hFAS and clinical conditions such as obesity, diabetes, and cancer. Thus, it has become an undeniably attractive pharmacological target. Until now, no crystal structure of the complete hFAS is available, hindering attempts to fully understand this protein. Using homology modeling, we built a model of the entire megasynthase, encompassing all of its domains, including the acyl carrier protein (ACP) and thioesterase (TE) mobile domains absent in the crystal structure of mammalian fatty acid synthase (FAS). On a second stage, we used data-driven protein-protein docking between the substrate shuttling domain ACP and every catalytic domain in the protein. We also propose sets of amino acids at the interface of each domain that we believe are important to favor the interaction between ACP and each domain of hFAS. After inspection, we validated each complex between ACP and MAT/KS/KR/DH/ER domains through classical molecular dynamics simulations and RMSd analysis. Additionally, we mapped the interactions between the residues at the active site of each catalytic domain and its intermediaries. In every docking, we ensured that the distance between catalytic residues and the intermediaries was maintained. Until now, there was not a complete 3D model of this megasynthase. This study is the first to present a homology model for the whole hFAS, including its two mobile domains and possible poses of ACP throughout the cycle of fatty acid biosynthesis, thus mapping obligatory checkpoints in its trajectory. Hence, we believe that these structural insights will allow for future studies of the catalytic mechanism of the overall hFAS.