A method and a system for acquiring diffusion magnetic resonance images with compensation of the effects of eddy currents induced by the diffusion weighting (DW) gradient pulses. Prescan data are first acquired using the same DW sequence to be used for imaging. The prescan data are used to obtain eddy current parameters that model the effects of DW-induced eddy currents under the exact conditions under which DW images are to be acquired. The DW imaging sequence is then slightly modified according to the eddy current parameters and used to acquire DW image data with the effects of DW-induced eddy currents compensated.