To provide a control apparatus for an internal combustion engine which can effectively utilize a scavenging effect while suppressing a torque difference in the internal combustion engine provided with a variable valve mechanism which makes a valve overlap period variable.When a scavenging effect utilization condition that the scavenging effect using exhaust pressure pulsation can be effectively utilized is established, a valve overlap period is set so as to overlap with a timing at which a trough of the exhaust pressure pulsation comes. In this occasion, a set value of the valve overlap period is limited such that an increase amount of a torque index value associated with the setting of valve overlap period does not exceed a predetermined permissible value.