In recent years the school enrolment rates of children aged 13–15 and 16–18 years have increased sharply in Indonesia, not only in urban but also in rural areas. Using various data sets spanning the years from 1993 to 2007, this paper investigates changes in factors associated with the enrolment of secondary school aged children in rural areas. It sheds light on the roles of gender and of neighbourhood and school characteristics, which have rarely been examined in the Indonesian context. The study finds that the disappearance of a gender gap in secondary enrolments between 1993 and 2007 contributed significantly to the rise in the overall enrolment rate. The findings also show that children living in wealthier communities and communities with a high proportion of enrolled children are more likely to attend school. Finally, various school characteristics are shown not to be strongly or consistently correlated with school enrolment.