Capturing of ducks at cages increased discomfort and stress. Herein, we tried to overcome this problem by addition of selenium in diet. We assessed the impact of organic selenium (0.4 gm/kg ration) supplementation on duck behaviour, welfare, thyroid hormones, and economic values. Forty-eight black Muscovy ducklings 3 weeks old, were reared in cage system and divided into two equal groups (control and Se-treated groups). No impact of the organic selenium supplementation on the feeding time, although the time was increased in the 10th week. The drinking bouts were significantly decreased (p < 0.05) in organic selenium treated group when compared with control group at finishing phase. The body weights (p < 0.01 in the 7th week, p < 0.001 in 8th, 9th and 10th weeks) and weight gains (p < 0.01 in 7th and 8th weeks) in the Se-treated group have been increased significantly compared to the control. Besides, the feed conversion ratio was highly decreased and relative growth rate was highly improved with organic selenium supplementation at both growing and finishing periods. Furthermore, the addition of organic selenium in caged ducks diet decreased the level of free thyroxine. On the economic basis, duck ration supplementation with organic selenium revealed the lowest cost/ kg weight gain, the highest economic return, net profit, and profitability index. Adding organic selenium to ration is important to display the duck’s fundamental needs and behavioural patterns, and to ensure their welfare, productivity and economic gain.