A fuel injection controller for an engine that injects fuel to an inlet passage in an upstream side of an inlet valve from a fuel injection unit, includes: a first calculator, configured to calculate a basic fuel injection quantity from the fuel injection unit based on an operating condition of the engine; a second calculator, configured to calculate a first direct transport rate of fuel directly transported into a cylinder of the fuel injected from the fuel injection unit when the inlet valve is closed; a third calculator, configured to calculate a second direct transport rate of fuel directly transported into a cylinder of the fuel injected from the fuel injection unit when the inlet valve is opened; and a corrector, configured to correct the basic fuel injection quantity based on the first direct transport rate and the second direct transport rate.