This longitudinal study examined how two externalising behaviour problems, attention-deficit hyperactivity disorder (ADHD) and conduct disorder (CDs), are associated over time with low motivation (MAS), and how these problems effect academic performance. In our cross-lagged analysis, we found reciprocal effects between ADHD symptoms and MAS between Grades 5 and 6. Both domains also negatively predicted later academic performance. With CDs and MAS, no cross-lagged effects were found, although both were correlated and very stable over time, and negatively predicted later academic performance. These different kinds of externalising problem behaviours seem to differ in the way in which they interact with students’ MAS and academic performance in the long term. Students with ADHD symptoms are likely to be more vulnerable to negative learning experiences and the development of MAS than students with CDs.