China has achieved high vaccination coverage under the Expanded Program on Immunization (EPI) in children 1-2 years of age. However, a knowledge gap exists regarding vaccination coverage and timeliness for children >2 years of age. As such, this study aimed to estimate coverage and timeliness for all EPI and selected non-EPI vaccines within a rural area of China. Immunization data for 5091 children, born between September 2003 and November 2015, were collected from vaccination cards obtained during sero-surveillance follow-up visits and/or from the Hunan immunization information system. For each dose of both EPI and non-EPI vaccines, vaccination coverage and timeliness were calculated, and temporal variations were examined across birth cohorts. We found coverage for EPI vaccines scheduled for <12 months was 97.1%-99.4%. However, for EPI vaccines scheduled at 6 years coverage was 44.4%-51.7%. The timeliness for EPI vaccines was generally poor, especially for EPI vaccines introduced after 2008 or scheduled for administration at ≥12 months, with a maximum of 35.4% of children vaccinated according to schedule. Despite this, we found increasing trends in vaccination coverage and improvements in timeliness for EPI vaccines. However, for non-EPI vaccines, we found only moderate increases, and in some cases decreases, in vaccination coverage. This study demonstrates the success and improvement of the Chinese immunization program, but also highlights some challenges to be addressed. We recommend that future changes in vaccine practice and policy should primarily focus on improving coverage and timeliness of vaccines introduced after 2008, and/or scheduled for administration ≥12 months.