Summary The objective of this study was to evaluate the effect of selenium (Se) supplementation on milk somatic cell count (SCC) in dairy cows. Twelve multiparous Holstein–Friesian cows were fed a diet containing a suboptimal Se concentration (<0.05 ppm, dry basis) starting 2 months before calving. Supplemented cows ( n = 6) received a single s.c. injection of barium selenate (1 ml/50 kg BW) 45 days prior to calving, whereas control group was kept unsupplemented. Twenty weeks after calving, two mammary quarters (right side) of each cow were challenged with 205 000 cfu/ml of Staphylococcus aureus (strain Newbould 305). Blood was collected bi‐weekly until day 150 of lactation for the analysis of blood glutathione peroxidase (GPx1; EC 1.11.1.9) activity. To re‐isolate the challenging pathogen and to evaluate SCC, aseptic milk samples were collected daily starting on the day of challenge, and finishing 7 days after inoculation. Unsupplemented cows had a lower activity of GPx1 through the experiment ( P < 0.001). Natural log SCC (lnSCC) was higher in unsupplemented than Se‐supplemented cows ( P = 0.04), showing evidence of significance after 5 days. Selenium supplementation of dairy cows fed a diet containing a suboptimal Se concentration, resulted in higher blood activity of GPx1, and lower mean lnSCC after an intramammary challenge with Staph. aureus .