We derive a mesoscopic theory of the Josephson junction from nonrelativistic scalar electrodynamics. Our theory reproduces the Josephson relations with the canonical current phase relation acquiring a weak second harmonic term, and it improves the standard lumped-element descriptions employed in circuit quantum electrodynamics by providing spatial resolution of the superconducting order parameter and electromagnetic field. By providing an ab initio derivation of the charge qubit Hamiltonian that relates traditionally free qubit parameters to geometric and material properties, we progress toward the quantum engineering of superconducting circuits at the subnanometer scale.