PurposeEddy currents might lead to image distortions in diffusion‐weighted echo planar imaging. A method is proposed to reduce their effects on double diffusion encoding (DDE) MRI experiments and the thereby derived microscopic fractional anisotropy (μFA).MethodsThe twice‐refocused spin echo scheme was adapted for DDE measurements. To assess the effect of individual diffusion encodings on the image distortions, measurements of a grid of plastic rods in water were performed. The effect of eddy current compensation on μFA measurements was evaluated in the brains of six healthy volunteers.ResultsThe use of an eddy current compensation reduced the signal variation. As expected, the distortions caused by the second encoding were larger than those of the first encoding, entailing a stronger need to compensate for them. For an optimal result, however, both encodings had to be compensated. The artifact reduction strongly improved the measurement of the μFA in ventricles and gray matter by reducing the overestimation. An effect of the compensation on absolute μFA values in white matter was not observed.ConclusionIt is advisable to compensate both encodings in DDE measurements for eddy currents. Magn Reson Med 77:328–335, 2017. © 2015 Wiley Periodicals, Inc.