The aim of this study was to examine the effects of Flavobacterium psychrophilum, a pathogen that is economically important in the aquaculture sector, on the neuroendocrine response of Oncorhynchus mykiss during a time course experiment with sampling at 0.5, 1, 2, 6, 10, and 30 days post injection (dpi). In the brain, serotonin (5HT) content increased in the infected group at all the measured time points, a similar pattern was observed for 5-hydroxyindole-3-acetic acid (5HIAA). Infected fish presented an increase in brain dopamine levels on day 0.5 and 1 dpi. A non-significant variation in noradrenaline levels was observed on all treatment days. Foregut 5-HT and 5-HIAA content in the infected group presented the highest 5-HT concentrations with 248.6 and 983.5 ng/g tissue at 0.5 dpi respectively. Midgut 5-HT and 5-HIAA levels presented the highest 5-HT concentrations, 486.9 ng/g tissue and 1006.4 ng/g tissue respectively, at the beginning of the experiment (0.5 dpi). 5-HT levels in the hindgut presented the highest concentrations with 233.9 ng/g tissue at 0.5 dpi, while 5-HIAA presented the highest concentrations, 690.5 ng/g tissue, at the same time point. After injection with F. psychrophilum the neuroendocrine response in rainbow trout was tissue dependent. Brain levels of 5HT and 5HIIA indicate that the neuroendocrine response increased together with dopamine following intramuscular infection. These increases are in line with reports from other authors, indicating an early response of catecholamines as neurotransmitters to stressful stimulus. In addition the intestinal response was also increased, implying that there could be a possible relationship between the serotonergic system at the intestinal level and the immune system.