Abstract Background National linked mortality and census data have not previously been available for Australia. We estimated education-based mortality inequalities from linked census and mortality data that are suitable for international comparisons. Methods We used the Australian Bureau of Statistics Death Registrations to Census file, with data on deaths (2011–2012) linked probabilistically to census data (linkage rate 81%). To assess validity, we compared mortality rates by age group (25–44, 45–64, 65–84 years), sex and area-inequality measures to those based on complete death registration data. We used negative binomial regression to quantify inequalities in all-cause mortality in relation to five levels of education [‘Bachelor degree or higher’ (highest) to ‘no Year 12 and no post-secondary qualification’ (lowest)], separately by sex and age group, adjusting for single year of age and correcting for linkage bias and missing education data. Results Mortality rates and area-based inequality estimates were comparable to published national estimates. Men aged 25–84 years with the lowest education had age-adjusted mortality rates 2.20 [95% confidence interval (CI): 2.08‒2.33] times those of men with the highest education. Among women, the rate ratio was 1.64 (1.55‒1.74). Rate ratios were 3.87 (3.38‒4.44) in men and 2.57 (2.15‒3.07) in women aged 25–44 years, decreasing to 1.68 (1.60‒1.76) in men and 1.44 (1.36‒1.53) in women aged 65–84 years. Absolute education inequalities increased with age. One in three to four deaths (31%) was associated with less than Bachelor level education. Conclusions These linked national data enabled valid estimates of education inequality in mortality suitable for international comparisons. The magnitude of relative inequality is substantial and similar to that reported for other high-income countries.