Abstract Mesopelagic fishes may contribute substantially to marine carbon export and sequestration. However, uncertainty in this contribution due to limited precision of mesopelagic biomass and bioenergetic rate estimates has not been thoroughly quantified for any study site. Datasets that can confront these challenges are rare, particularly for comparing fish-mediated carbon flux to other biological carbon pump pathways. Using data from a unique three-ship expedition in spring 2021 in the subarctic Northeast Atlantic Ocean, we compare carbon transported by adult fish, zooplankton, and sinking particles, and calculate uncertainty in the relative contribution of fishes. Results indicate biomass- and bioenergetic-based uncertainty contributed roughly equally to variance in estimated carbon transport. The plausible range of mesopelagic fish carbon flux spans an order of magnitude: 1.6–21 mg C m−2 d−1 to 200 m depth and 0.52–9.6 mg C m−2 d−1 to 500 m. Fishes contributed ∼0.52%–18% at 200 m to the total biological carbon pump, and ∼0.43%–13% at 500 m. Of the fish-mediated carbon transport to 200 m, ∼8%–30% is sequestered on climate-relevant time scales (>100 years). This reinforces that carbon transport should not be conflated with carbon sequestration. These findings have implications for prioritizing future empirical measurements, evaluating trade-offs in fisheries management, and understanding the role of fishes in the biological carbon pump.