Students often feel isolated when they do blended learning courses and they do not always have the necessary skills to work on their own. Blended learning courses need to be thoughtfully planned to actively involve students in the learning processes. Cooperative learning is an active teaching strategy that can assist students to engage in online and blended courses and is known to promote self-directed learning. The communities of inquiry framework is often used as a framework to design blended learning. In this study, we focused on an additional dimension of the communities of inquiry framework, namely courses learning presence, which is closely linked with self-directed learning skills. In this basic qualitative study, semi-structured interviews were conducted with post-graduate Mathematics Education students (n = 8) to establish their experience of the cooperative blended learning course. Data were coded and analysed using a deductive approach. The aim of this article is to describe how self-directed learning as learning presence can be enhanced through a cooperative blended learning course. The findings showed that the use of cooperative learning was a useful strategy to promote self-directed learning as learning presence. Furthermore, matters relating to motivation as a component of self-directed learning were incorporated into the design of the course, such as allowing students to manage their own learning, making the learning experience enjoyable, and providing encouraging feedback. Aspects of the course design that assisted in promoting self-directed learning as learning presence included the use of authentic tasks, allowing students to develop and apply their own learning strategies, and providing students with the opportunity to socially construct knowledge.