An apparatus for controlling an EGR valve, includes: a measurement unit to measure at least one operation condition of an engine system; a fresh air amount setting unit to set a target amount of fresh air based on the operation condition; a fresh air amount sensor to measure a current amount of fresh air introduced through an intake line; a control calculation unit to set a signal for controlling an opening degree of the EGR valve so that the current amount of fresh air follows the target amount of fresh air; and an identifier to simulate an input and an output of the engine system, and output engine system input-output sensitivity which is a ratio of a change rate of the current amount of fresh air to a change rate of the opening degree of the EGR valve.