Mechanical ventilation systems account for a significant portion of building energy use, particularly due to fan operation. While modern designs increasingly incorporate energy-saving features such as heat recovery and demand-driven control, choosing the right system topology and control strategy is difficult in the early-stage planning. This paper extends a mixed-integer linear programming (MILP) approach to simultaneously optimise duct sizing, fan and damper placement. Five control strategies—ranging from constant air volume to an optimal configuration with centralised control over distributed components—are compared in terms of power consumption and life-cycle costs. The results of a case study show that more sophisticated control strategies, especially those that adapt pressure or decentralise control elements, offer cost and energy savings. The proposed method provides fast, optimal solutions, supporting informed decision-making during the critical preplanning phase of ventilation system design. It contributes to more energy-efficient building services and supports SDGs 9 and 11.