Selenium (Se) is an essential micronutrient required for normal development and antioxidant protection. Oxidative stress induced by stressful conditions has been shown to be reduced by dietary Se supplementation. However, replacing fishmeal, an important source of Se, with ingredients of plant origin usually results in decreased Se content in aquafeeds. The objective of the study was hence to assess the impact of dietary Se supplementation by an inorganic or organic source on the antioxidant defense system of rainbow trout (Oncorhynchus mykiss) juveniles fed practical plant-based feeds under normal or chronic stress conditions. Fish (initial mean weight: 42 ± 2 g) were maintained under normal (25 fish/tank, dissolved oxygen: 7.9 mg/l) or stressful conditions combining decreased water quality with hypoxia and increased stocking density (50 fish/tank, dissolved oxygen: 5.9 mg/l) for 12 weeks at 17 °C. Rainbow trout juveniles were fed three plant-derived protein-based diets containing 0.5 mg Se/kg diet supplemented or not with 0.3 mg Se/kg diet supplied as sodium selenite or Se-enriched yeast, Selsaf®. The apparent digestibility coefficients (ADC) of dry matter, protein, ash and Se were improved by Se-enriched yeast supplementation while the ADC of Se was reduced by sodium selenite supplementation and the ADC of dry matter, starch, energy, ash and phosphorus were reduced by chronic stress exposure. Dietary Se supplementation had no significant impact on growth performance contrary to chronic stress exposure which led to decreased final body weight and feed intake. Total Se content of fish was increased by both dietary Se supplementations but to a larger extent with Se-enriched yeast. Fish fed Se-enriched yeast displayed increased hepatic selenomethionine content and decreased muscle anisidine value. Blood glutathione content was reduced by chronic stress exposure. While hepatic catalase activity and transcript expression were increased by chronic stress exposure, both hepatic and renal glutathione peroxidase (GPX) activity and hepatic transcript expression of gpx1b2 and gpx4a2 were decreased in non-Se supplemented fish. These results suggest the necessity to supplement plant-based diets with Se for rainbow trout juveniles, independently of chronic stress exposure and highlight the superiority of organic form of Se to fulfil the dietary Se requirement and sustain the antioxidant status of fish.