Theoretical calculations are an effective strategy to complement and understand the experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach are performed to reveal for the first time the electron dynamics for the charge separation of pyrene-functionalized middle-sized Au70S20(PH3)16 and large-sized Au108S24(PR3)16 (R = H, CH3, C2H5, C6H5) clusters. The proposed mechanism uncovers an ultrafast and irreversible photoinduced charge transfer from the gold nanocluster (GNC) unit to the pyrene derivative in all cases. By a Fourier transform analysis of the dynamics, the effect of vibronic couplings is highlighted. The Au108S24(PPh3)15PPh2Pyr system exhibits the best performance for charge separation.