A valve characteristic controller for an engine including variable valve actuation mechanisms, one for a first valve and another for a second valve, to vary the opening and closing timings of the valves. The controller executes main control to calculate a target timing of the first valve in accordance with an operation state of the engine and has the corresponding variable valve actuation mechanism adjust the timing of the first valve to the target timing. Further, the controller executes sub-control to calculate a target timing of the second valve based on a target valve overlap amount and the actual timing of the first valve and has the corresponding variable valve actuation mechanism adjust the valve timing of the second valve to the target timing. The main control is executed on the one of the two variable valve actuation mechanisms having a lower response speed.