We have investigated the superconducting gap of optimally doped Ba(Fe$_{0.65}$Ru$_{0.35}$)$_2$As$_2$ by angle-resolved photoemission spectroscopy (APRES) using bulk-sensitive 7 eV laser and synchrotron radiation. It was found that the gap is isotropic in the $k_x$-$k_y$ plane both on the electron and hole Fermi surfaces (FSs). The gap magnitudes of two resolved hole FSs show similar $k_z$ dependences and decrease as $k_z$ approaches $sim$ 2$pi$/$c$ (i.e., around the Z point) unlike the other Fe-based superconductors reported so far, where the superconducting gap of only one hole FS shows a strong $k_z$ dependence. This unique gap structure can be understood in the scenario that the $d_{z^2}$ orbital character is mixed into both hole FSs due to the finite spin-orbit coupling between almost degenerate FSs and is reproduced by calculations within the random phase approximation including the spin-orbit coupling.