Abstract Understanding and accurately characterizing energy dissipation mechanisms in civil structures during earthquakes is an important element of seismic assessment and design. The most commonly used model is attributed to Rayleigh. This paper proposes a systematic approach to quantify the uncertainty associated with Rayleigh’s damping model. Bayesian calibration with embedded model error is employed to treat the coefficients of the Rayleigh model as random variables using modal damping ratios. Through a numerical example, we illustrate how this approach works and how the calibrated model can address modeling uncertainty associated with the Rayleigh damping model.