A fuel filter assembly includes a housing connected between a fuel tank and a high-pressure pump supplying fuel to a common rail injecting the fuel pumped from the fuel tank to an engine through a pipeline; a filter incorporated in the housing to filter impurities in the fuel pumped from the fuel tank; and a center pipe disposed in an inner space of the housing in a longitudinal direction of the housing and substantially enclosed by the filter, wherein bottom portion of the center pipe is spaced from bottom portion of the housing, the center pipe discharging filtered fuel collected in the bottom portion of the center pipe by suction of the high-pressure pump.