Fused filament fabrication (FFF) is a 3D printing method that is attracting increased interest in the development of miniaturized electrochemical sensor systems due to its versatility, low cost, reproducibility, and capability for rapid prototyping. A key component of miniaturized electrochemical systems is the reference electrode (RE). However, reports of the fabrication of a true 3D-printed RE that exhibits stability to variations in the sample matrix remain limited. In this work, we report the development and characterization of a 3D-printed Ag|AgCl|gel-KCl reference electrode (3D-RE). The RE was constructed using a Ag|AgCl wire and agar-KCl layer housed in a watertight 3D-printed acrylonitrile butadiene styrene (ABS) casing. The novel feature of our electrode is a 3D-printed porous junction that protects the gel electrolyte layer from chloride ion leakage and test sample contamination while maintaining electrical contact with the sample solution. By tuning the 3D printing filament extrusion ratio (k), the porosity of the junction was adjusted to balance the reference electrode potential stability and impedance. The resulting 3D-RE demonstrated a stable potential, with a potential drift of 4.55 ± 0.46 mV over a 12-h period of continuous immersion in 0.1 M KCl, and a low impedance of 0.50 ± 0.11 kΩ. The 3D-RE was also insensitive to variations in the sample matrix and maintained a stable potential for at least 30 days under proper storage in 3 M KCl. We demonstrate the application of this 3D-RE in cyclic voltammetry and in pH sensing coupled with electrodeposited iridium oxide on a gold electrode. Our method offers a viable strategy for 3D printing a customizable true reference electrode that can be readily fabricated on demand and integrated into 3D-printed miniaturized electrochemical sensor systems.