Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), which cause significant worldwide losses in aquaculture. Juvenile rainbow trout are particularly susceptible to F. psychrophilum infection, the main external clinical signs of which are extensive necrotic myositis and ulcerative lesions. Despite the economic relevance of this pathogen in aquaculture, little is known about the molecular mechanisms underlying F. psychrophilum infection and pathogenesis. In this study, cultured skeletal muscle cells from rainbow trout (Oncorhynchus mykiss) were co-incubated with the virulent strain of F. psychrophilum JIP02/86 (ATCC 49511). Trypan blue exclusion analysis at 48h post-incubation revealed decreased cellular viability. Direct bacteria-myoblast contact was found a key factor in inducing F. psychrophilum cytotoxicity. Apoptosis was characterized by nuclear DNA fragmentation, decreased plasma membrane integrity, increased caspase activity, and the proteolytic cleavage of poly(ADP-ribose)polymerase-1 (PARP-1). Moreover, bacterial infection induced an early inhibition of NF-κB signaling, as well as a differential expression of the pro- and anti-apoptotic genes, bax and bcl-2. These findings suggest that F. psychrophilum induces rainbow trout muscle apoptosis through the modulation of the NF-κB signaling as a mechanism for nutrient acquisition and survival.