Children’s emergent leadership is an important but often ignored component of peer-led collaborative learning. Existing research suggests that emergent leadership develops when children are given the autonomy and space to regulate group dynamics on their own, which often assists the group to achieve better outcomes within the collaborative activities. However, it is less known whether the emergence of child leadership also promotes deeper and more connected reasoning during collaborative learning. This current study, by coding emergent leadership and relational thinking from two sets of small group discussions (25 in total), revealed that over time, children exhibited more leadership and relational thinking in the second collaborative discussion than their first one. In addition, intellectual leadership moves, rather than organizational leadership moves, were positively related to generation of relational thinking. We discuss the implications of the study to help children, particularly minority children from underserved communities, to developing leadership and relational thinking through participating in intellectually stimulating collaborative discussions.