RNA-seq data from Neocalanus flemingeri pre-adult (CV) individuals collected during oceanographic cruises the northern Gulf of Alaska with stations in Prince William Sound and additional stations spanning the inner shelf to outer shelf gradient along the Seward Line. Collections were quickly live-sorted for N. flemingeri pre-adult (CV) under the microscope and immediately preserved for RNA-seq. The rapid sorting of live plankton can lead to misidentifications given the presence of closely-related congeners, thus species verification using the cytochrome c oxidase subunit 1 (mtCOI) sequence as a filter is recommended.