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The article is devoted to extension of boundary element method (BEM) for solving coupled equations in velocity and induced magnetic field for time dependent magnetohydrodynamic (MHD) flows through a rectangular pipe. The BEM is equipped with finite difference approach to solveMHDproblem at high Hartmann numbers up to 106. In fact, the finite difference approach is used to approximate partial derivatives of unknown functions at boundary points respect to outward normal vector. It yields a numerical method with no singular boundary integrals. Besides, a new approach is suggested in this article where transforms 2D singular BEM's integrals to 1D nonsingular ones. The new approach reduces computational cost, significantly. Note that the stability of the numerical scheme is proved mathematically when computational domain is discretized uniformly and Hartmann number is 40 times bigger than length of boundary elements. Numerical examples show behavior of velocity and induced magnetic field across the sections. [ABSTRACT FROM AUTHOR]