We present an explicit time domain boundary element method (TDBEM) scheme with moving window technique for short-range wake field simulations of long accelerator structures. The proposed scheme is formulated by Kirchhoff's boundary integral equation of the scattered electromagnetic field in interior region problems. Implementation of a moving window technique in the framework of TDBEM is achieved by taking into account the causality and the retardation properties of the boundary integral equation. A parallelization algorithm for this moving window implementation is also proposed. The proposed TDBEM code with the moving window technique is applied to several practical examples of long accelerator structures. Numerical results obtained with the TDBEM code are compared with those of several finite integration codes.