Quantum tunneling conductance of molecular junctions originates from the charge transport through the π-orbitals (π-transport) and the σ-orbitals (σ-transport) of the molecules, but the σ-transport can not be observed due to the more rapid decay of the tunneling conductance in the σ-system compared to that in the π-system. Here, we demonstrate that dominant σ-transport can be observed in π-conjugated molecular junctions at the sub-nanometer scale using the scanning tunneling microscope break junction technique (STM-BJ). We have found that the conductance of meta-connected picolinic acid, which mainly occurs by σ-transport, is ∼35 times higher than that of its para-isomer, which is entirely different from what is expected from π-transport through these systems. Flicker noise analysis reveals that the transport through the meta-connection exhibits more through-bond transport than the para-counterpart and density functional theory (DFT) shows that the σ-system provides the dominant transport path. These results reveal that the σ-electrons, rather than the π-electrons, can dominate charge transport through conjugated molecular junctions at the sub-nanometer scale, and this provides a new avenue toward the future miniaturization of molecular devices and materials.