The engineering of pulsed electric field (PEF) reactors using carbon materials as the electrode was carried out to fundamentally eliminate the concern about the release of metallic ions into the treatment solution. PEF treatment using carbon cloth with a textile structure showed a strong inactivation effect on the inactivation Escherichia coil in a batch-type reactor. We also developed two continuous-flow-type PEF reactors: one allowed the treatment solution to flow parallel and the other perpendicular to the surface of the electrode. When the two reactors were compared, the latter showed higher sterilization capability. The effects of decreasing the flow rate of the treatment solution and increasing the electric field intensity on the inactivation of E. coli by PEF treatment were investigated. Although both improved the E. coif inactivation efficiency, the latter showed higher inactivation efficiency and a smaller increase in the temperature of the treatment solution. From the viewpoint of engineering for the pasteurization of liquid food, increasing the electric field intensity was more effective in the PEF treatment than decreasing the flow rate of the treatment solution. The continuous-flow-type PEF reactor with the carbon cloth electrode was applied to the pasteurization of sake, and although the sake yeast and Lactobacillus homohiochu in the sake were not inactivated to undetectable levels, they were significantly inactivated by continuous-flow PEF treatment.