A control device includes a controller configured to: obtain a driving condition and an actual value of a controlled amount of an engine; use a transformed engine model to calculate an estimate value of a future controlled amount, from the obtained driving condition and a candidate value of an operation amount for controlling the controlled amount, the transformed engine model in which an activation function of each neuron is transformed using a linear inequality function having a binary variable, the transformed engine model for which a weight coefficient, bias, and upper and lower limits of an input/output variable of the each neuron are set based on an engine model that has a multilayer neural structure and the activation function of a ReLU structure, receives the driving condition and operation amount as input, and predicts dynamic characteristics of the engine; determine a value of the operation amount, based on error between the calculated estimate value and a target value of the controlled amount identified from the driving condition.