This paper proposes an IEC 61850-based centralized busbar differential protection scheme, in which data desynchronization between intelligent electronic devices (IEDs) leads to differential current errors. As the differential current errors could result in erroneous operation of the centralized busbar differential protection, data desynchronization should be compensated for. The main causes of data desynchronization are subdivided into measurement timing and time synchronization errors. In this paper, the first-order Lagrange interpolation polynomial is used to compensate for measurement timing errors and the voltage angle differences between IEDs are used to compensate for time synchronization errors. The centralized busbar differential protection is tested using a real-time digital simulator and IEC 61850-based IEDs, which are implemented with the MMS-EASE Lite library and Smart Grid Infrastructure Evaluation Module. The test results show that the data desynchronization compensation can significantly reduce differential current errors, and thus prevent erroneous operation of the IEC 61850-based centralized busbar differential protection.