In this study we investigate the causes of low secondary school enrollment in Indonesia despite near universal primary school attendance. We then find that attrition during the transition between primary and junior secondary education levels is the main cause. We investigate the causes of attrition using a longitudinal household survey dataset. Firstly, household welfare level is a significant determinant of the low enrollment. Secondly, children from Muslim families have a significantly lower probability of continuing to the secondary level. Thirdly, children in areas with relatively abundant employment opportunities have a higher probability of giving up schooling. Fourthly, girls have a significantly lower chance of continuing. The policy implications of our results point to, among other things, the need for refocusing government education spending and scholarship programs to target those who go missing from the education system after completing primary education.