Gold nanorods (AuNRs) with an aspect ratio of 2.33 or 3.16 were self-assembled onto 1,6-hexanedithiol-modified gold electrodes based on covalent interaction at a solution temperature of 35 °C. The formation of the 1,6HDT/AuNR bilayers as a function of the nanorods’ adsorption time was studied by atomic force microscopy and quartz crystal microbalance, whereas their physical properties and chemical bonding were studied by contact angle and FT-IRRAS spectroscopy measurements. It was found that both types of nanorods were covalently bonded to the Au-1,6HDT-SAM modified electrodes in an end topography and with a high surface density. The electrochemical properties of the Au-1,6HDT-AuNR modified electrodes, as a function of the nanorods’ adsorption time, were studied by cyclic voltammetry, square wave voltammetry, and electrochemical impedance spectroscopy using [Fe(CN)6]3−/4−as the redox probes. The highest enhancement of the electrical current in the cyclic voltammograms was recorded at the Au-1,6HDT-AuNR modified electrodes for 7 h of chemisorption of 2.33 aspect ratio rods or 15 h of chemisorption of 3.16 aspect ratio rods. The high decrease of the apparent charge-transfer resistance upon nanorod self-assembly suggests a charging of the rods by the [Fe(CN)6]3−/4− in solution and electron transfer across them. Moreover, the variation of the tunneling parameter β suggests that the electron tunneling process through the 1,6HDT molecules is more efficient at the electrodes modified with bilayers containing short rods (β = 0.78 ± 0.08 Å−1/per methylene unit) than at the electrodes modified with bilayers containing long rods (β = 0.84 ± 0.10 Å−1/per methylene unit). The self-assembly of the AuNRs in an end-bonding topography with a high surface coverage restored almost completely the electronic communication that was entirely blocked by the preceding 1,6HDT layer.