Self-configuration of physical cell identity (PCI) is a key feature for the long term evolution advanced (LTE-A) network. The PCI is used to identify the different cells in the system, becoming an essential cell configuration parameter. Considering the uncoordinated deployments of the evolved Node B (eNodeB) and the limited number of PCI, the PCI assignment for cells would be quite complex. This paper presents and puts forward a graph theory based centralized PCI self-configuration scheme (GT-PCIS). The PCI self-configuration problem is mapped to the well-known minimum spanning tree (MST) problem in order to optimize the PCI reuse distance and decrease the multiplexing interference throughout the entire network. The proposal provides a greedy search to make the locally optimal selection of PCI at each stage, and to achieve a global optimum. To demonstrate the algorithm validity, performances of GT-PCIS and manual configuration are evaluated. Simulation results show that the proposed GT-PCIS outperforms other configuration algorithms even under the condition of severe PCI deficiency.