This study characterized associations between annually scaled thermal indices and annual heat stress illness (HSI) morbidity outcomes, including heat stroke and heat exhaustion, among active-duty soldiers at ten Continental U.S. (CONUS) Army installations from 1991 to 2018. We fit negative binomial models for 3 types of HSI morbidity outcomes and annual indices for temperature, heat index, and wet-bulb globe temperature (WBGT), adjusting for installation-level effects and long-term trends in the negative binomial regression models using block-bootstrap resampling. Ambulatory (out-patient) and reportable event HSI outcomes displayed predominately positive association patterns with the assessed annual indices of heat, whereas hospitalization associations were mostly null. For example, a one-degree Fahrenheit (°F) (or 0.55°C) increase in mean temperature between May and September was associated with a 1.16 (95% confidence interval [CI]: 1.11, 1.29) times greater rate of ambulatory encounters. The annual-scaled rate ratios and their uncertainties may be applied to climate projections for a wide range of thermal indices to estimate future military and civilian HSI burdens and impacts to medical resources.