This study explores the extent to which structural stigma (which encompasses sociocultural and institutional constraining factors) is associated with sexual orientation disparities in healthcare service and prescription medicine use. Using the responses to the 2017 Australian Marriage Law Postal Survey, we use the regional percentage of votes against legalising same-sex marriage as a measure of structural stigma. We then map these results to Census-linked-administrative data, including 83,519 individuals in same-sex relationships - one of the largest administrative datasets to date where individuals in same-sex relationships are identified. Controlling for regional and individual-level confounders, we find that structural stigma is associated with increased use of nervous system medications (which largely comprise antidepressants) but reduced GP visits for both females and males in same-sex relationships. More regional stigma is also associated with reduced use of pathology services and anti-infective prescriptions for males in same-sex relationships. Altogether, our results suggest that individuals in same-sex relationships living in stigmatised regions are in poorer health but are less likely to access primary healthcare.