A control apparatus of an engine including intake and exhaust valves and a variable valve timing mechanism for varying open and close timings is provided. The apparatus includes a processor configured to execute an increasing amount controlling module for performing a fuel amount increase control in which a fuel injection amount is increased to decrease an exhaust gas temperature, and a valve controlling module for controlling, via the variable valve timing mechanism, an overlapping period in which the intake and exhaust valves are both opened on intake stroke. When the increasing amount controlling module performs the increase control, based on an increase of a temperature of the exhaust gas in the increase control, the valve controlling module determines whether a protection for an exhaust system component is required, and if the protection is determined to be required, the valve controlling module shortens the overlapping period.