The assemblage structure, abundance, biomass, and vertical distribution of juvenile reef fishes in the offshore pelagic habitat of the northern Gulf of Mexico are described as part of the NOAA-supported Offshore Nekton Sampling and Analysis Program. The results presented here are from a 3-month, continuous sampling series in 2011 in which discrete depth strata from 0 to 1500 m were sampled using a 10-m2 MOCNESS midwater trawl. This is the first study to examine pelagic juvenile reef fish distributions across the entire oceanic northern Gulf of Mexico seaward of the continental shelf break after the Deepwater Horizon Oil Spill. During this series, 87,407 specimens were collected, of which 838 were reef fishes, representing seven orders, 30 families and 119 species. The faunal composition of pelagic juvenile reef fishes was diverse and well mixed, with no discernable spatial structure with respect to water masses and solar cycle. Seventy-nine percent of the pelagic juvenile reef fishes were collected in the epipelagic and the dominant families were Congridae, Carangidae, Tetraodontidae, and Acanthuridae. Species richness, biomass, and frequency of occurrence of pelagic juvenile reef fishes was greatest between 0-200 m and decreased with depth. Data from the assemblage structure, abundance, biomass, and vertical distribution of pelagic juvenile reef fishes collected from this cruise series will contribute to the lack of knowledge regarding the dispersal dynamics and coastal-connectivity of these fishes in the northern Gulf of Mexico.