Objective India has experienced a substantial increase in the coverage of routine childhood vaccines in recent years. However, a large fraction of these vaccines is not delivered in a timely manner, i.e., at the recommended age. Further, substantial disparities exist in both coverage and timeliness across states. We aim to quantify the changes in coverage and timeliness of routine childhood vaccination in India over time, their variation across states, and changes in these variations over time. Methods We used data from two rounds of India’s National Family Health Surveys, NFHS-3 (2005–06) and NFHS-4 (2015–16) on bacille Calmette–Guerin vaccine (BCG), three doses of diphtheria, pertussis, and tetanus vaccine (DPT1, DPT2, DPT3), and measles-containing vaccine (MCV). We used the Turnbull estimator to estimate the cumulative distribution function (CDF) of administering each vaccine by a certain age while accounting for two-sided censoring in the survey data. We then used these estimated CDFs to calculate coverage and timeliness at the national and state levels. Findings At the national level, both vaccination coverage and timeliness estimates increased from NFHS-3 to NFHS-4 for all vaccines. The increase in timeliness ranging from 27.3% for DPT3 to 74.0% for MCV continued to be lower than coverage, ranging from 75.3% (95% CI 57.7–87.2) for DPT3 to 74.0% (95% CI 42.2–33.0) for MCV, for all vaccines. Cross-state variation in timeliness was greater than the variation in coverage. Variation in both timeliness and coverage reduced from NFHS-3 to NFHS-4. However, this reduction was greater for timeliness than for coverage. Conclusions A large fraction of the children in India receive vaccines later than the recommended age thereby keeping them exposed to vaccine-preventable diseases. Interventions that specifically focus on improving the timely delivery of vaccines are needed to improve the overall effectiveness of the routine immunization program.