A valve operation controller for an internal combustion engine is provided for optimally setting a valve opening timing and a valve closing timing for an intake valve in accordance with an operating state of the internal combustion engine to improve the fuel efficiency and power of the internal combustion engine, eliminate fuel stagnation in the intake valve and sticking of the intake valve with its valve seat, and reduce the cost and weight. The valve operation controller controls open/close operations of exhaust valves (EV1, EV2) and first and second intake valves (IV1, IV2) arranged in one cylinder (4). An electromagnetic valve operating mechanism (5) electromagnetically opens/closes the first intake valve (IV1). A cam type valve operating mechanism (6) opens/closes the second intake valve (IV2) with an intake cam (11) arranged on a cam shaft (10) driven in synchronism with rotation of the internal combustion engine (3). The cam type valve operating mechanism (6) can generate a cylinder flowage within a combustion chamber of the cylinder (4). An ECU (2) controls operations of the electromagnetic valve operating mechanism (5) and the cam type valve operating mechanism (6).