A nanometric revolution is underway, promising technical innovations in a wide range of applications and leading to a potential boost in environmental discharges. The propensity of nanoparticles (NPs) to be transferred throughout trophic chains and to generate toxicity was mainly assessed in primary consumers, whereas a lack of knowledge for higher trophic levels persists. The present study focused on a predatory fish, the European eel (Anguilla anguilla) exposed to gold NPs (AuNPs; 10 nm, polyethylene glycol-coated) for 21 d at 3 concentration levels in food: 0 (NP0), 1 (NP1), and 10 (NP10) mg Au kg(-1). Transfer was assessed by Au quantification in eel tissues, and transcriptomic responses in the liver and brain were revealed by a high-throughput RNA-sequencing approach. Eels fed at NP10 presented an erratic feeding behavior, whereas Au quantification only indicated transfer to intestine and kidney of NP1-exposed eels. Sequencing of RNA was performed in NP0 and NP1 eels. A total of 258 genes and 156 genes were significantly differentially transcribed in response to AuNP trophic exposure in the liver and brain, respectively. Enrichment analysis highlighted modifications in the immune system-related processes in the liver. In addition, results pointed out a shared response of both organs regarding 13 genes, most of them being involved in immune functions. This finding may shed light on the mode of action and toxicity of AuNPs in fish.