Electrokinetic flows are generally analyzed, assuming isothermal conditions even though such situations are hard to be achieved in practice. In this paper, the flow of a symmetric electrolyte in a charged nanochannel subjected to an axial temperature gradient is investigated using molecular dynamics simulations. We analyze the relative contribution of the Soret effect, the thermoelectric effect, and the double layer potential in the electrical double layer for various surface charges and temperature gradients. We find the flow driven by thermal gradient is analogous to electroosmotic flow. The thermophoretic motion of the electrolyte is significant for negative surface charge than the positive surface charge. The vibrational spectrum of graphene is calculated to delineate the effect of the surface charge polarity on the observed thermophoretic motion of the electrolyte. A unique structure of interfacial water layer is observed for the positive and negative surface charges. We attribute the presence of these structures to the differences in water-carbon interactions existing for various surface charge polarity. For an applied thermal gradient in the range 2.6 K nm-1 to 8 K nm-1, we observe a continuous net flow with average velocities reaching up to 9.4 m s-1 inside the channel for a negative surface charge of -0.101 C m-2. The results indicate that in a charged graphene-based nanochannel, temperature gradients can be employed to induce streaming current, depending on the relative influence of the Soret effect and the double layer potential. © 2020 IOP Publishing Ltd.