Although the importance of primary schools in the long term is of interest in educational effectiveness research, few studies have examined the long-term effects of schools over the past decades. In the present study, long-term effects of primary schools on the educational positions of students 2 and 4 years after starting secondary education are investigated. Moreover, it is examined which school factors play a role in this process. We specifically investigated whether effective primary schools make a difference in the long term. This study uses data from the longitudinal SiBO project, which followed 6,000 pupils in primary education in Flanders, Belgium, and has follow-up data during secondary education. Two-level models and cross-classified multilevel models show that primary schools have long-term effects on the educational positions of students in secondary education.