The gilthead sea bream (Sparus aurata) is a marine fish of great importance for Mediterranean aquaculture. The recent appearance of of a Nervous Necrosis Viral reassortant strain started to pose a serious threat to sea bream hatcheries, as it is able to infect larvae and juveniles of this species. We therefore performed a time-course RNA-seq analysis on 21-day old fish gilthead sea bream larvae experimentally infected with a NNV, to understand the molecular mechanisms and responses triggered during viral infection.