The safe, highly effective measles vaccine has been recommended globally since 1974, yet in 2017 there were over 17 million measles cases and 83,400 deaths in children under 5 years old; over 99% of both occurred in low- and middle-income countries (LMICs). Globally comparable, annual, local estimates of routine first-dose measles-containing vaccine (MCV1) coverage are critical for understanding geographically precise immunity patterns, progress toward Global Vaccine Action Plan (GVAP) targets, and high-risk areas amidst COVID-19-related vaccination programme disruptions. We generated annual estimates of routine childhood MCV1 coverage at 5 × 5-kilometre and second administrative levels from 2000 to 2019 in 101 LMICs, quantified geographic inequality, and assessed vaccination status by geographic remoteness. After widespread MCV1 gains from 2000 to 2010, coverage regressed in over half of districts between 2010 and 2019, leaving many LMICs far from the GVAP goal of 80% coverage in all districts by 2019. MCV1 coverage was lower in rural than urban locations, although a larger proportion of unvaccinated children overall lived in urban locations; strategies to provide essential vaccination services should address both geographic contexts. These results provide a tool for decision-makers to strengthen routine MCV1 immunisation programmes and provide equitable disease protection for all children.