A two-component charge transfer (CT) hydrogel has been derived from a supramolecular heteroassembly of a pyrene amino acid conjugate (PyHisOH, donor) with a 4-chloro-7-nitrobenzofurazan (NBD-Ox, acceptor) derivative in aqueous medium. The mechanical stiffness, as well as the thermal stability of the CT hydrogels largely depend on the relative ratios of donor and acceptor units as well as on their overall concentration. Moreover, the gel-to-sol transition is found to be susceptible to various external stimuli such as heat, pH, metal ions, etc. Circular dichroism and morphological investigation reveal the formation of left-handed helical fibers in the CT gel network. XRD studies show the lamellar packing of the interactive units in the 3D network of the CT hydrogel. The determination of different rheological parameters confirms the viscoelastic as well as the thixotropic nature of the CT gel. Furthermore, the CT gel is employed for turn-on sensing of biogenic thiols, cyan fluorescence was observed with cysteine/homocysteine, while blue fluorescence with glutathione. Nucleophilic attack at the NBD moiety leads to the formation of thermodynamically stable amino-linked derivatives for cysteine or homocysteine and kinetically controlled thiol-linked adduct for glutathione. Thus, the current system presents a unique opportunity, where a CT hydrogel sample is involved for discriminating biogenic thiols via specific chemodosimetric interactions.