Arsenic (As) in groundwater severely harms global economic development by affecting growth and productivity of agricultural crops that causes human health risk. The comparative influence of silicon (Si) and selenium (Se) to modulate pigments levels, photosynthetic parameters using LI-6400XT Portable Photosynthesis System and carbohydrate metabolism under arsenate (As-V) stress in rice cv. MTU-1010 were evaluated. As(V) stress significantly decreased chlorophyll-a (32% on an average), chlorophyll-b (58% on an average), total chlorophyll (46% on an average), fluorescence intensity (31% on an average),, carotene (39% on an average), xanthophyll (33% on an average), Hill activity (47% on an average) and the photosynthetic parameters viz., intercellular-CO2-concentration (52% on an average), net photosynthesis (54% on an average), transpiration rate (36% on an average) and stomatal conductance (38% on an average) in the test seedlings. As(V) + Si treatments enhanced the said parameters more than As(V) + Se treatments in rice seedlings. Sugar contents viz., reducing (85% on an average) and non-reducing sugar (61% on an average) were increased but starch content (57% on an average) was decreased in As(V) treated seedlings. The activities of carbohydrate metabolizing enzymes were increased, while sucrose synthase activity was decreased due to As(V) toxicity in the test seedlings. Co-application of Si and As(V) as well as Se and As(V) showed ameliorative effects on the said parameters but more potential effect was observed under combined application of Si and As(V) in rice seedlings. Thus, the present study is focused to highlight the comparative capability of Si and Se to ameliorate the As induced toxic effects on chloroplast pigments, photosynthetic activities and sugar metabolism in rice seedlings which will be an effective approach to develop possible strategies in As contaminated agricultural soil to improve normal growth and productivity of rice plants.