Abstract An ecosystem-based flow analysis model was used to study carbon transfer from primary production (PP) to mesopelagic fish via three groups of copepods: detritivores that access sinking particles, vertical migrators, and species that reside in the surface ocean. The model was parameterized for 40°S to 40°N in the world ocean such that results can be compared with recent estimates of mesopelagic fish biomass in this latitudinal range, based on field studies using acoustic technologies, of ∼13 Gt (wet weight). Mesopelagic fish production was predicted to be 0.32% of PP which, assuming fish longevity of 1.5 years, gives rise to predicted mesopelagic fish biomass of 2.4 Gt. Model ensembles were run to analyse the uncertainty of this estimate, with results showing predicted biomass >10 Gt in only 8% of the simulations. The work emphasizes the importance of migrating animals in transferring carbon from the surface ocean to the mesopelagic zone. It also highlights how little is known about the physiological ecology of mesopelagic fish, trophic pathways within the mesopelagic food web, and how these link to PP in the surface ocean. A deeper understanding of these interacting factors is required before the potential for utilizing mesopelagic fish as a harvestable resource can be robustly assessed.