Flunixin meglumine is a highly efficacious nonsteroidal anti‐inflammatory drug commonly used in equine medicine and especially in performance horses. Recently, a new transdermal flunixin meglumine product has been approved for use in cattle. Although not currently approved for use in the horse, the convenience of this product may prove appealing for use in horses, warranting study. Six horses were administered a single transdermal dose of 500 mg and blood and urine samples collected for up to 96 h post‐administration. Serum for determination of thromboxane concentrations and whole blood samples was collected at various time and challenged with lipopolysaccharide, calcium ionophore, or methanol to induce ex vivo synthesis of eicosanoids. Concentrations of flunixin, 5‐OH flunixin, and eicosanoids were measured using LC‐MS/MS and non‐compartmental pharmacokinetic analysis performed on concentration data. Serum concentrations of flunixin and 5‐OH flunixin were above the limit of quantitation at 96 h post‐administration in both serum and urine. The mean (range) for Cmax, Tmax and the terminal half‐life were 515.6 (369.7–714.0) ng/ml, 8.67 (8.0 12.0) h, and 22.4 (18.3–42.5) h, respectively. Following transdermal administration, based on effects on eicosanoid synthesis, flunixin meglumine inhibited cyclooxygenase 1 and 2 and 15‐lipooxygenase activity, with anti‐inflammatory effects lasting for 24–72 h.