An apparatus for controlling the operation of an engine based on the pressure in an intake manifold. If a change in the pressure in the intake manifold is equal to or less than a predetermined value during a predetermined period within the period from the time when a voltage source is turned on to the time when a starter is turned on, the pressure in the intake manifold is detected and stored. If the engine is not in the start mode, the rate of fuel supply is increased based on an atmospheric pressure detection value. Based on the comparison between the atmospheric pressure value and a predetermined value, a passage for bypassing a throttle valve is opened and closed to control the idling of the engine.