Regional base hospitals require high performance to maintain their functions even in the event of a large earthquake. This study proposes a method to design the parameters of a linear quadratic regulator (LQR) for a seismic control device aiming at improving the resilience of a medical facility. First, fault tree analysis was conducted to reveal the factors that hinder the recovery of medical facilities. The fragility curves and recovery-time probability models were constructed for medical devices based on the literature review and the interviews with medical device manufacturers. Using these models, the recovery curve, which is the relationship between the functional level and time, can be evaluated for the building–medical equipment system under an assumed earthquake ground motion. We propose to minimize the time to recover up to the defined functional level, 95% or 80%, in designing parameters for an LQR control system. The effectiveness of the proposed control design method was investigated for a building with a control device installed on its top floor, and it was confirmed that the proposed method improved the resilience performance compared with the conventional control method.