A control apparatus of an engine including an intake valve, an exhaust valve, and a variable valve timing mechanism for varying open and close timings of at least one of the intake and exhaust valves, is provided. The control apparatus includes a processor configured to execute a valve controlling module for performing, via the variable valve timing mechanism, a valve overlap in which the intake and exhaust valves are both opened on intake stroke of the engine, and a temperature estimating module for estimating a temperature of exhaust gas at a given location in the exhaust system by estimating a temperature increase of the exhaust gas caused by afterburn and accounting for the temperature increase, the afterburn occurring due to fresh air blowing through a cylinder of the engine to an exhaust system during the valve overlap.