Many parents move from rural China to urban areas in search of job opportunities, and leave their children behind to be raised by relatives. We aimed to assess the immunisation coverage, including the 1:3:3:3:1 vaccine series (one dose of Bacilli Chalmette–Guérin vaccine; three doses of live attenuated oral poliomyelitis vaccine; three doses of diphtheria, tetanus and pertussis combined; three doses of hepatitis B vaccine; and one dose of measles-containing vaccine), in children aged 12–72 months and identify the determinants of immunisation uptake among left-behind children in Hubei Province, Central China, in 2014. In this cross-sectional study using the World Health Organization's cluster sampling technique, we surveyed 1368 children from 44 villages in 11 districts of Hubei Province. The socio-demographic and vaccination status data were collected by interviewing primary caregivers using a semi-structured questionnaire and reviewing the immunisation cards of the children. Univariate and multivariate analyses were used to identify the determinants of complete vaccination and age-appropriate vaccination. For each dose of the five vaccines, the vaccination coverage in the left-behind and non-left-behind children was >90%; however, the age-appropriate vaccination coverage for each vaccine was lower in left-behind than in non-left-behind children. For the five vaccines, the fully vaccinated rate of left-behind children were lower than those of non-left-behind children (89·1%, 92·7%; P = 0·013) and age-appropriate immunisation rate of left-behind children were lower than those of non-left-behind children (65·7%, 79·9%; P < 0·001). After controlling for potential confounders, we found that the parenting pattern, annual household income and attitude of the primary caregiver towards vaccination significantly influenced the vaccination status of children. Moreover, we noted a relatively high prevalence of delayed vaccination among left-behind children. Hence, we believe that the age-appropriate immunisation coverage rate among left-behind children in rural areas should be further improved by delivering and sustaining primary care services.