The Rapid Refresh (RAP) is an hourly updated regional meteorological data assimilation/short-range model forecast system running operationally at NOAA/National Centers for Environmental Prediction (NCEP) using the community Gridpoint Statistical Interpolation analysis system (GSI). This paper documents the application of the GSI three-dimensional hybrid ensemble–variational assimilation option to the RAP high-resolution, hourly cycling system and shows the skill improvements of 1–12-h forecasts of upper-air wind, moisture, and temperature over the purely three-dimensional variational analysis system. Use of perturbation data from an independent global ensemble, the Global Data Assimilation System (GDAS), is demonstrated to be very effective for the regional RAP hybrid assimilation. In this paper, application of the GSI-hybrid assimilation for the RAP is explained. Results from sensitivity experiments are shown to define configurations for the operational RAP version 2, the ratio of static and ensemble background error covariance, and vertical and horizontal localization scales for the operational RAP version 3. Finally, a 1-week RAP experiment from a summer period was performed using a global ensemble from a winter period, suggesting that a significant component of its multivariate covariance structure from the ensemble is independent of time matching between analysis time and ensemble valid time.