A method and system for correcting a fuel injection amount that injects fuel may include applying a current value for injecting a target fuel amount and injecting fuel under a driving condition in which fuel injection is blocked; determining a frequency analysis value for a pressure signal of the fuel pressure rail when the fuel is injected; determining a fuel amount difference corresponding to a difference value between the frequency analysis value and a reference frequency analysis value stored in a data storage in advance; and correcting a current value of the injector which is applied to inject the target fuel amount to remove the fuel amount difference.