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Introduction Context-specific cost-effectiveness thresholds (CETs) informed by societal willingness to pay (WTP) are crucial for healthcare resource allocation in low- and middle-income countries. This study investigated WTP for health per quality-adjusted life year (QALY) in Bhutan.Methods A WTP survey was conducted alongside the 2023 National Health Survey in Bhutan, sampling 1869 households. Using contingent valuation, respondents assigned monetary values to three hypothetical scenarios: 1 year of cancer symptom-free life, 1 year of perfect health and 5 years of perfect health. We used generalised linear regression to estimate WTP, controlling for demographic, socioeconomic and health-related factors, as well as elicitation methods. Multilevel analyses examined WTP variations within and between districts.Results WTP estimates were 76 836 Bhutanese ngultrum (BTN) (0.26 times gross domestic product (GDP) per capita; 95% CI: 71 397 to 82 275) for a year without cancer symptoms, 104 381 BTN (0.35 times GDP per capita; 95% CI: 96 405 to 112 357) for 1 QALY and 235 237 BTN (0.78 times GDP per capita; 95% CI: 218 674 to 251 800) for 5 QALYs. WTP variations were driven by within-district individual characteristics, particularly income and education, rather than between-district differences.Conclusion Minimal between-district WTP variations support a national-level CET for Bhutan. However, WTP-based CETs would be biased upward by wealthier and more educated groups. This bias could justify expensive technologies that strain public resources in Bhutan’s government-funded healthcare system.