Provided are a molecular electronic device and a method of fabricating the molecular electronic device. The molecular electronic device includes a substrate, an organic dielectric thin film formed over the substrate, a molecular active layer formed on the organic dielectric thin film and having a charge trap site, and an electrode formed on the molecular active layer. The organic dielectric thin film may be immobilized on the electrode or a Si layer by a self-assembled method. The organic dielectric thin film may include first and second molecular layers bound together through hydrogen bonds. An organic compound may be self-assembled over the substrate to form the organic dielectric thin film. The organic compound may include an M′-R-T structure, where M′, R and T represent a thiol or silane derivative, a saturated or unsaturated C1 to C20 hydrocarbon group which is substituted or unsubstituted with fluorine (F), and an amino(—NH2) or carboxyl (—COOH) group, respectively.