Thermal discomfort is persistent yet under-documented in Nigerian secondary hospitals. These facilities serve the largest cross-section of the population but lack systematic empirical evidence. This study investigates how outdoor climate and ward building configuration determine indoor thermal comfort across six government-owned hospitals in Kwara State. A mixed-methods design integrated ten years of climatic data with in-situ measurements of temperature, humidity, and air velocity alongside 305 user questionnaires. Mahoney table analysis classified the six hospitals into three micro-climatic zones: hot-humid (Sobi, Centre Igboro), hot-dry (Jebba), and warm-comfort transition (Omu-Aran, Offa, Share). Open wards constituted the largest ward type (48.2%). Natural ventilation served 56.4% of ward spaces. Afternoon operative temperatures averaged 31.4°C during the harmattan period, exceeding the adaptive comfort boundary of 31.8°C for spaces with functional window control. Among occupants without operable windows (48.9% of respondents), afternoon temperatures exceeded the prescriptive ASHRAE limit of 26°C by 5.6°C. Chi-square analysis found no statistically significant association between ward layout and ventilation type (χ²(9) = 14.725, p = 0.099). One-way ANOVA confirmed no statistically significant difference in comfort satisfaction across hospitals (F(5,299) = 1.49, p = 0.193, η² = 0.024), indicating shared design or operational characteristics rather than facility-specific deficiencies. Effective remediation requires a climate-responsive design framework calibrated to the three identified zones and revision of national standards to mandate performance-based thermal comfort outcomes.