For any graph, Weisfeiler and Leman assigned the smallest matrix algebra which contains the adjacency matrix of the graph. The coherent configuration underlying this algebra for a graph $\Gamma$ is called the coherent configuration of $\Gamma$, denoted by $\mathcal{X}(\Gamma)$. In this paper, we study the coherent configuration of circular-arc graphs. We give a characterization of the circular-arc graphs $\Gamma$, where $\mathcal{X}(\Gamma)$ is a homogeneous coherent configuration. Moreover, all homogeneous coherent configurations which are obtained in this way are characterized as a subclass of Schurian coherent configurations.