This paper presents a new method that uses the equivalent-input-disturbance (EID) approach to estimate the wind load of a seismically isolated building. To verify the control performance of wind-resistant design methods and devices, wind-load data are important for structural design of skyscrapers. However, wind loads cannot be measured directly and is usually estimated based on structural responses. Previous studies focused on a building model in which the damping coefficient is proportional to a linear combination of mass and stiffness (referred to as Rayleigh damping). These existing methods cannot be directly applied to a seismically isolated building because its damping is not Rayleigh damping. Moreover, a structural model usually contains uncertainties caused by modeling errors that cause the degradation of estimation performance. To solve these problems, this paper combines the EID approach with a robust control strategy to design a wind-load estimator for a seismically isolated building with uncertainties. First, the configuration of an EID-based estimation system is shown. Next, a robust wind-load estimator is presented. Then, simulations are carried out to demonstrate the validity of the presented method using wind-load data obtained from a wind-tunnel test. An 11-degree-of-freedom model of a seismically isolated building is used for numerical verification. The results show that, even if a model contains 20% uncertainties, the presented method accurately estimates the wind load of a seismically isolated building.