We have investigated electron tunneling through two one-dimensional (1D) molecular junctions based on first-principles simulations using the density functional theory combined with the non-equilibrium Green’s functions methodology. The first junction, composed of left and right carbyne wire electrodes with a sodium atom in between, is atomically thin. The second one is quasi-one-dimensional (quasi-1D) and consists of two single-wall carbon nanotube electrodes, closed on the tips and again a sodium atom in the scattering region. Although the bridging atom bonds weakly to the electrodes in both systems, it strongly affects the electronic transport properties, such as electron transmission, current–voltage relation, differential conductance, density of states and eigenchannels. This is demonstrated by comparing with the results obtained from the corresponding systems for both the 1D and the quasi-1D junctions in the absence of the central sodium atom. The revealed transport properties are sensitive to the molecular geometry. This helps future molecular electronic device design.