Objectives of these studies were to determine the effects of flunixin meglumine (FM) administration on early embryonic mortality and circulating PG and cortisol concentrations in transported and non-transported cows. Cows (n = 483) from 3 locations were used to evaluate the effects of transportation and FM approximately 14 d after AI on the establishment of pregnancy and serum concentrations of progesterone, PGF metabolite (PGFM), and cortisol. Treatments were transport (n = 129), transport + FM (n = 128), no transport (n = 130), and no transport + FM (n = 96). Multiparous cows (n = 224) were used at 2 locations, and nulliparous cows (n = 259) were used at 1 location. The no transport + FM treatment was used at only 2 locations. Flunixin meglumine (approximately 1.1 mg/kg of BW; i.m.) was administered before the cows were separated into transportation groups. Transportation included 4 to 6 h of transportation, without calves, via semitractor trailer. Nontransported cows remained penned, with their calves in adjacent pens, during the same period as the transported cows. Blood samples were collected from all cows before and after treatment and, at 2 locations, approximately 3 h after the onset of treatment. Location affected AI pregnancy rate (P < 0.01). Treatment effects, although not significant (P = 0.16), were of a magnitude to be considered practically important. Cows that received transportation + FM tended (P = 0.07) to have greater AI pregnancy rates (74%) than those that did not receive FM (66%), irrespective of transportation. Cortisol concentration was greater (P < 0.05) for transported cows than for nontransported cows. Cows receiving FM had greater (P < 0.05) AI pregnancy rates than non-FM cows (71 vs. 61%, respectively). Cows receiving transportation had lower (P < 0.01) mean PGFM concentrations than nontransported cows (45.4 vs. 54.6 pg/mL, respectively), and cows receiving FM had lower (P < 0.01) mean PGFM concentrations than non-FM cows (39.4 vs. 60.6, respectively). We conclude that transportation of cows approximately 14 d after AI increased serum cortisol concentrations but did not affect AI pregnancy rates. However, treatment of cows with FM increased AI pregnancy rates, irrespective of whether they were transported.