Pulsatile brain motion is considered to be an important mechanical link between blood and cerebrospinal fluid (CSF) dynamics. Like many severe brain diseases, different types of hydrocephalus are associated with impairment of these dynamics. In this work a cine displacement-encoded imaging method employing stimulated echoes (DENSE) and a three-dimensional (3D) segmented echo-planar imaging (EPI) readout for brain motion measurements in all three spatial directions is presented. Displacement-encoded data sets of 12 healthy volunteers were analyzed with respect to reproducibility, periodicity, and intra- as well as intersubject physiological consistency. In addition, displacement values were compared with data derived from phase-contrast (PC) velocity measurements in a subset of all measured subjects. Using DENSE, displacements as low as 0.01 mm could be detected and observation of the 3D pulse pressure wave propagation was possible. Among other parameters, peak displacements in the central brain regions were measured: feet–head (FH): thalamus (0.13 ± 0.01 mm); right–left (RL): thalamus (0.06 ± 0.01 mm); and anterior–posterior (AP): caudate nucleus (0.05 ± 0.01 mm).