This study proposes a low-cost, portable paper-fluidic vertical flow assay bacterium counter with high accuracy. We designed sensors with low fabrication costs based on e-beam evaporation and three-dimensional printing based on the impedance measurement principle. Interdigitated (IDT) electrodes were coated on the filter membrane by e-beam evaporation with a shadow mask. We could print wafer-scale frames with low melting temperature three-dimensional-printing materials for confining liquid bacterial samples within the IDT sensing region. This novel fabrication technique significantly reduced the chip’s cost to less than 1% of that of silicon-based chips. Two equivalent circuit models were proposed for different concentration ranges to analyze the principle of paper-based impedance bacterial sensors. We proposed an improved model based on the Randles model for low concentrations by considering the leaky double-layer capacitor effect and spherical diffusion from the nano-structural electrodes of the gold-coated filter membrane. The phenomenon in which charge transfer resistance, Rct, declines at high concentration ranges was found and explained by the pearl chain effect. The pearl effect could cause a false-negative at high concentrations. We modeled the pearl chain effect as an R and C, connected parallel to the low-concentration model. When users properly applied both models for analyses, this sensor could quantitatively measure cell concentrations from 400 to 400 M per milliliter with superior linearity.