Dietary fish oil‐derived n‐3 PUFA supplementation can increase muscle mass, reduce oxygen demand during physical activity, and improve physical function (muscle strength and power, and endurance) in people. The results from several studies conducted in animals suggest that the anabolic and performance‐enhancing effects of n‐3 PUFA are at least in part transcriptionally regulated. The effect of n‐3 PUFA therapy on the muscle transcriptome in people is unknown. In this study, we used muscle biopsy samples collected during a recently completed randomized controlled trial that found that n‐3 PUFA therapy increased muscle mass and function in older adults to provide a comprehensive assessment of the effect of n‐3 PUFA therapy on the skeletal muscle gene expression profile in these people. Using the microarray technique, we found that several pathways involved in regulating mitochondrial function and extracellular matrix organization were increased and pathways related to calpain‐ and ubiquitin‐mediated proteolysis and inhibition of the key anabolic regulator mTOR were decreased by n‐3 PUFA therapy. However, the effect of n‐3 PUFA therapy on the expression of individual genes involved in regulating mitochondrial function and muscle growth, assessed by quantitative RT‐PCR, was very small. These data suggest that n‐3 PUFA therapy results in small but coordinated changes in the muscle transcriptome that may help explain the n‐3 PUFA‐induced improvements in muscle mass and function.