Using deep models to classify brain functional networks (BFNs) for the auxiliary diagnosis and treatment of brain diseases has become increasingly popular. However, the unexplainability of deep models has seriously hindered their applications in computer-aided diagnosis. In addition, current explanation methods mostly focus on natural images, which cannot be directly used to explain the deep model for BFN classification. In this paper, we propose a concept-level causal explanation method for BFN classification called CLCEM. First, CLCEM employs the causal learning method to extract concepts that are meaningful to humans from BFNs. Second, it aggregates the same concepts to obtain the contribution of each concept to the model output. Finally, CLCEM adds the contribution of each concept to make a diagnosis. The experimental results show that our CLCEM can not only accurately identify brain regions related to specific brain diseases but also make decisions based on the concepts of these brain regions, which enables humans to understand the decision-making process without performance degradation.