This paper proposes a fully 3D-printed electromagnetic (EM) microfluidic sensor using rectangular substrate integrated waveguide (SIW) for liquid complex permittivity characterization. The proposed microfluidic sensor is fabricated with a novel additive manufacturing process in which dielectric and conductive inks are simultaneously 3D-printed, allowing high print quality, rapid prototyping, and arbitrary geometry. The fabrication process removes the need for post-printing sintering and cleaning steps that require harmful chemicals. The sensor structure is composed of upper and lower metal plates and a series of cylindrical metal side vias. Since the electric field is high at the center of the SIW cavity in <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\textit {TE}_{101}$ </tex-math></inline-formula> mode, a cylindrical dielectric sample container in the form of a microwell is built into the center of the SIW cavity to maximize the perturbation of the liquid under test (LUT). The application of LUT samples to the microwell results in a change in the resonance frequency and peak attenuation from which the LUT sample is characterized. Ethanol-water mixtures are used as LUTs for validation. The proposed sensor has been verified numerically and experimentally, reducing the resonant frequency from 3.750 GHz to 3.862 GHz by increasing the ethanol volume fraction from 0% to 100%. The sensor showed good sensitivity of 0.345% and a stable frequency change was observed over five measurement repetitions. To the best of our knowledge, this article presents the first fully 3D-printed SIW microfluidic sensor and demonstrates its ability to detect and characterize the liquid complex permittivity.