This investigation evaluated, in broiler chickens Pectoralis and Gastrocnemius muscles, the effect of the dietary supplementation with sodium selenite (0.3 ppm) versus selenomethionine (0.3 ppm), on the fatty acids composition, lipids indices, and enzymes indexes for desaturase, elongase, and thioesterase. The selenium reduced, in both muscles, the content of atherogenic fatty acids, C14:0 and C16:0, while it increased the C18:1 level. On the other hand, selenium increased, in both muscles, the content of C18:3n3 and EPA, but not DPA and DHA. No selenium effect was detected for PUFA/SFA, n-6, n-3, n-6/n-3, and atherogenic and thrombogenic indices. As for the enzyme indexes, a selenium effect is only detected for thioesterase. Taken together, the results highlight the potential effect of dietary selenium, mainly selenomethionine, in the modulation of the composition of fatty acids in chicken meat, in particular, reducing the content of atherogenic fatty acids and increasing the health promoting n-3 PUFA.