The Bigeye Thresher is caught globally as target and bycatch in commercial and small-scale pelagic longline, purse seine, and gillnet fisheries. Most catch is taken as bycatch of commercial pelagic fleets in offshore and high-seas waters (Camhi et al. 2008). It is also captured in coastal longlines, gillnets, trammel nets, and sometimes trawls, particularly in areas with narrow continental shelves (Camhi et al. 2008, Martinez-Ortiz et al. 2015, Temple et al. 2019, Fauconnet et al. 2019). The Bigeye Thresher generally spends time near the surface at night where it is exposed to fisheries capture but it likely has some refuge during the day, when it generally dives to greater depths than those at which most commercial tuna fleets operate.

The species is often retained for the quality meat and the fins (Clarke et al. 2006a, Clarke et al. 2006b, Dent and Clarke 2015, Fields et al. 2018), unless regulations prohibit retention. Under-reporting of catches is likely in pelagic and domestic fisheries (Dent and Clarke 2015). The species is highly valued by big-game recreational fishers, and although many practice catch and release, recreational fishing could be a threat due the likelihood of post-release mortality that has been estimated for the congener Common Thresher as 78% for tail-hooked and 0% for mouth-hooked animals (i.e. all mouth-hooked animals survived) (Camhi et al. 2008, Sepulveda et al. 2015). For commercial fisheries, at-vessel hooking mortality for the Bigeye Thresher is high with between 49 and 68% of individuals caught found to be dead on haulback (Coelho et al. 2011, IOTC 2016).