Glyphosate is a commonly used agrochemical active substance co-formulated in glyphosate-based herbicides (GBHs) whose environmental safety is still a subject of debate in the European Union. We evaluated the effects of acute sublethal exposure to glyphosate on rainbow trout by measuring changes in their metabolic and hemato-immunologic functions and their ability to survive a viral challenge. Juvenile fish were exposed for 96 h to 500 μg L−1 of glyphosate through the active substance alone or two GHBs, Roundup Innovert® and Viaglif Jardin®, and fish were then infected with the infectious hematopoietic necrosis virus. Red and white blood cell counts (RBCC and WBCC), as well as several enzymatic activities (citrate synthase, CS; cytochrome-c oxidase, CCO; lactate dehydrogenase, LDH; glucose-6-phosphate dehydrogenase, G6PDH; acetylcholinesterase, AChE), were measured 96 h after chemical contamination (S1), and 96 h post-viral infection (S2). Mortality rates were monitored, and virus titers at the mortality peaks and seropositivity of the survivors were analyzed at 60 days post-viral infection (S3). Cumulative mortalities, viral titers, and seropositivity induced by virus infection were similar among conditions. Hematological analysis revealed significant increases of 30% for RBCC for Roundup at S1, and of 22% for WBCC at S2. No changes were observed in metabolic enzyme activities at S1. At S2, CCO and G6PDH activities were significantly higher than controls in all the chemically contaminated groups (+61 to 62% and +65 to 138%, respectively). LDH and AChE activities were increased for the Viaglif (p = 0.07; +55%) and for glyphosate and Roundup conditions (p < 0.05, +62 to 79%), respectively. Rainbow trout acutely exposed to glyphosate or GBHs presented no major physiological changes. Viral infection revealed disruptions, potentially modulated by co-formulants, of hematological and metabolic parameters, showing that it is essential to consider the stressful natural environment of fish in the chemical assessment.