A method of and an apparatus for diagnosing an engine system are provided. An apparatus for diagnosing an engine system including a continuous variable valve duration (CVVD) apparatus and an exhaust gas recirculation (EGR) apparatus may include: an accelerator pedal position sensor detecting a position of an accelerator pedal; a brake pedal position sensor detecting a position of a brake pedal; a vehicle speed sensor detecting a speed of a vehicle; an intake pressure sensor detecting an intake pressure; and a controller determining whether a fuel cut condition is satisfied and determining whether the CVVD apparatus and an EGR valve is in a failure state when the fuel cut condition is satisfied.