In the present study, zinc oxide (ZnO) nanorods (NRs) with a hexagonal structure have been synthesized via a hydrothermal method assisted by microwave radiation, using specialized cardboard materials as substrates. Cardboard-type substrates are cost-efficient and robust paper-based platforms that can be integrated into several opto-electronic applications for medical diagnostics, analysis and/or quality control devices. This class of substrates also enables highly-sensitive Raman molecular detection, amiable to several different operational environments and target surfaces. The structural characterization of the ZnO NR arrays has been carried out by X-ray diffraction (XRD), scanning electron microscopy (SEM) and optical measurements. The effects of the synthesis time (5–30 min) and temperature (70–130 °C) of the ZnO NR arrays decorated with silver nanoparticles (AgNPs) have been investigated in view of their application for surface-enhanced Raman scattering (SERS) molecular detection. The size and density of the ZnO NRs, as well as those of the AgNPs, are shown to play a central role in the final SERS response. A Raman enhancement factor of 7 × 105 was obtained using rhodamine 6 G (R6G) as the test analyte; a ZnO NR array was produced for only 5 min at 70 °C. This condition presents higher ZnO NR and AgNP densities, thereby increasing the total number of plasmonic “hot-spots”, their volume coverage and the number of analyte molecules that are subject to enhanced sensing.