ABSTRACT Background Globally, most people with head and neck cancers (HNCs) are diagnosed with advanced‐stage disease. HNC diagnostic stage has multifactorial explanations, with the role of health system factors not yet fully investigated. Methods HNC centres ( n = 18) from the HEADSpAcE Consortium were surveyed via a bespoke health system questionnaire covering a range of factors. Centres were compared using the least square means for the presence/absence of each health system factor to their proportion of advanced‐stage HNC. Results Health system factors associated with lower proportion in advanced‐stage diagnosis were formal referral triaging (14%, 95% CI‐0.26, −0.03), routine monitoring of time from referral to diagnosis (16%, 95% CI‐0.27, −0.05), and fully publicly funded systems (17%, 95% CI‐0.29, −0.06). Several health systems factors had no routinely available data. Conclusions Through identifying and monitoring health systems factors associated with lower proportions of advanced stage HNC, interventions could be developed, and systems redesigned, to improve early diagnosis.