The Hokkaido Eastern Iburi earthquake (M JMA = 6.7) occurred on September 6, 2018, in the Hokkaido corner region where the Kurile and northeastern Japan island arcs meet. We relocated aftershocks of this intraplate earthquake immediately after the main shock by using data from a permanent local seismic network and found that aftershock depths were concentrated from 20 to 40 km, which is extraordinarily deep compared with other shallow intraplate earthquakes in the inland area of Honshu and Kyushu, Japan. Further, we found that the aftershock area consists of three segments. The first segment is located in the northern part of the aftershock area, the second segment lies in the southern part, and the third segment forms a stepover between the other two segments. The hypocenter of the main shock, from which the rupture initiated, is located on the stepover segment. The centroid moment tensor solution for the main shock indicates a reverse faulting, whereas the focal mechanism solution determined by using the first-motion polarity of the P wave indicates strike-slip faulting. To explain this discrepancy qualitatively, we present a model in which the rupture started as a small strike-slip fault in the stepover segment of the aftershock area, followed by two large reverse faulting ruptures in the northern and southern segments.