Porous 2D-covalent organic frameworks (COF) that are assembled axially through weak π-stacking interactions can provide reticular charge transport channels while playing host to kinetically stabilized reactive molecular redox-states. Here we demonstrate the above paradigm by constructing a host-guest supramolecular charge transfer (CT) assembly using photoactive anthraquinone-based crystalline COF as an acceptor while incarcerating electron donor N,N-dimethylaniline (DMA) inside it. Employing femtosecond broadband transient absorption spectroscopy in combination with electron paramagnetic resonance (EPR) studies, we show that the CT occurs rapidly within <110 femtoseconds after photoexcitation, subsequently leading to long-lived charge separation with 13% quantum efficiency at room temperature. Photoinduced EPR signature of the long-lived confined DMA cation radical confirms the disparate regions of charge localization while 1H-13C correlation experiments using solid-state NMR spectroscopy enumerate the packing of the amines inside the host-guest COF assembly. Our work demonstrates the potency of rationally designed charge transport pathways in supramolecular assemblies for efficient charge separation which if optimally tuned should pave the way for COF-based photocatalytic reaction centres.