Variations in temperature throughout the reproductive tract have been noted in many species. A recent study found the cervix-rectum temperature differential (CR-TD) in cattle was related to fertility. The present study aimed to assess the CR-TD in mares around the time of ovulation and relate it to embryo recover. Over 52 cycles, mares were inseminated with a fertile stallion and embryo recovery was undertaken on Day 7 post ovulation. Further 10 control mares were not inseminated. Rectal and cervical temperatures were measured using a precision thermometer on four or five occasions: the day of deslorelin administration and insemination, the day before ovulation, the day of ovulation (Day 0), the day after ovulation and, for inseminated mares, before embryo recovery on Day 7. One-way ANOVA showed that the CR-TD was significantly lower on the day of ovulation in the 36 positive cycles, in which an embryo was recovered, versus the 16 in which the embryo flush was negative (0.21 ± 0.17 vs. 0.40 ± 0.09°C; p < 0.001). Control cycles showed equivalent CR-TD to positive (0.13 ± 0.22 vs. 0.21 ± 0.17°C; p = 0.196) but not negative cycles (0.13 ± 0.22 vs. 0.40 ± 0.09°C; p < 0.001). A positive embryo recovery was associated with lower CR-TDs from the time of insemination and deslorelin to the day after ovulation compared to the day of embryo flushing (RM ANOVA; p < 0.001; Pairwise comparisons; p ≤ 0.01, in all cases). Rectal or cervical temperatures per se showed no significant differences between positive, negative or control cycles at any time point. In conclusion, a thermoregulatory process occurs close to ovulation which results in a lower CR-TD in cycles that produced an embryo versus those which did not. Further characterisation of TDs within the reproductive tract of the mare would increase our understanding of the conditions required for optimum fertility.