In this study, we investigated the diving behavior of sei whales relative to the vertical distribution of their potential prey in the western North Pacific during the summer of 2013. Acoustic time-depth transmitters were attached to two sei whales for 10.2 and 32.0 h, respectively. The vertical distribution and density (expressed as the volume backscattering strength, SV) of their potential prey were recorded by an echosounder. Diving behavior was classified into two shapes: U-shaped and V-shaped. For both individuals, U-shaped diving was associated with higher SV values than V-shaped diving and the frequency of U-shaped diving increased from late afternoon until sunset. During the daytime, dense scattering layers (presumably zooplankton) were distributed at approximately 40 m and they then migrated toward the surface around sunset. The diving depth of the whales followed the diel migration of the scattering layers and the diving was concentrated in these layers when the density became high. The results of this study indicate that sei whales change their diving depth and shapes in response to the diel vertical migration of their potential prey.