This report describes the two component self-assembly of π-capped amino acid hydrogelators (serine (S), aspartic acid (D), glutamic acid (E) or lysine (K)) prepared from pyrene (Py) based donor and naphthalenediimide (NDI) based acceptor molecules. The co-assembly can be triggered to form hydrogels by varying the pH conditions and the major driving forces behind the hydrogelation were found to be the formation of a strong charge-transfer (CT) complex and hydrogen bonding interactions at suitable pH conditions. The NDI-Py blends with matched donor/acceptor amino acid pairs undergo self-assembly under acidic pH conditions, whereas the blend (NDI-S + Py-K) with a mismatched amino acid pair forms a stable hydrogel under physiological pH conditions. UV-Vis, FTIR and rheological studies clearly indicate the formation and the stability of these CT-induced hydrogels. These hydrogels are of nanofibrous morphology with an average diameter of about 6-9 nm as evidenced by TEM analysis. In addition, this novel NDI-Py mixed component system exhibited good biocompatibility towards PC3 cells. Overall, since hydrogels based on CT-mediated two-component assemblies are very rare, our newly discovered NDI-Py hydrogels provide chemical insights into the design of a CT-induced hydrogelator and might facilitate various applications in biomedical engineering.