The reproducibility of the electrical characteristics of molecular junctions has been notoriously low. This paper describes a method to construct tunnel junctions based on self-assembled monolayers (SAMs) by forming reversible electrical contacts to SAMs using top-electrodes of a non-Newtonian liquid-metal (GaOx/EGaIn) stabilized in a microfluidic-based device. A single top-electrode can be used to form up to 15–25 junctions. This method generates SAM-based junctions with highly reproducible electrical characteristics in terms of precision (widths of distributions) and replicability (closeness to a reference value). The reason is that this method, unlike other approaches that rely on cross-bar or nano/micropore configurations, does not require patterning of the bottom-electrodes and is compatible with ultra-flat template-stripped (TS) surfaces. This compatibly with non-patterned electrodes is important for three reasons. i) No edges of the electrodes are present at which SAMs cannot pack well. ii) Patterning requires photoresist that may contaminate the electrode and complicate SAM formation. iii) TS-surfaces contain large grains, have low rms values, and can be obtained and used (in ordinary laboratory conditions) within a few seconds to minimize contamination. The junctions have very good electrical stability (2500 current-voltage cycles and retained currents for 27 h), and can be fabricated with good yields (≈78%).