Stejneger's beaked whales were hunted in a Japanese fishery, along with Cuvier’s beaked whales. They are not presently the main targets of any hunt.

In the past, some individuals were taken in the Japanese salmon driftnet fishery in the Sea of Japan and in driftnets off the west coast of North America. Entanglement in fishing gear, especially gillnets in deep water, is probably the most significant threat.

This species, like other beaked whales, is likely to be vulnerable to loud anthropogenic sounds, such as those generated by navy sonar and seismic exploration (Cox et al. 2006).

As a cold water species, Stejneger’s beaked whale may be vulnerable to the effects of climate change as ocean warming may result in a contraction of the species range as it tracks the occurrence of its preferred water temperatures (Learmonth et al. 2006). The effect of such changes in range size on this species is unknown.

Evidence from stranded individuals of several similar species indicates that they have swallowed discarded plastic items, which may eventually lead to death (e.g. Scott et al. 2001); this species may also be at risk.