Environmental heat stress has a deleterious impact on farm animal reproductive performance. The purpose of this study was to see how the addition of melatonin affected the efficacy of the superovulation regimen in goats in hot climatic conditions. Sixteen Shiba goats were synchronized and divided into two equal groups (n = 8, each): the melatonin group, which received a single S/C dose of melatonin, and a control group, treated with one ml of corn oil only. Ultrasonographic assessment of ovarian structures (Graafian follicles; GFs and corpus lutea; CLs) morphometry and hemodynamics were performed during the estrous phase of the superovulation (D0) and at day7 after ovulation (D7) of the superovulation regimen. The peripheral reproductive hormones were measured, and microRNAs were characterized. The mean diameter and the total-colored area of GFs during the D0 were significantly (P˂0.05) higher in the melatonin group (5.42 ± 0.11 mm and 1592.20 ± 45.26 pixels, respectively) compared to the control group (4.62 ± 0.12 mm and 1052.55 ± 29.47 pixels, respectively). Concentrations of LH and E2 increased significantly (P˂0.05) in the melatonin group (1.06 ± 0.06 ng/ml and 46.34 ± 2.77 pg/ml, respectively) compared to the control group (0.75 ± 0.12 ng/ml and 29.33 ± 1.89 pg/ml, respectively). At D7, the melatonin-received goats attained greater values in the mean count (6.75 ± 0.33, P˂0.005), diameters (6.08 ± 0.12 mm, P˂0.01), and total-colored area (17137.30 ± 128.53 pixels, P˂0.01) of detected CLs and progesterone concentrations (4.08 ± 0.24 ng/ml) compared to control goats (4.00 ± 0.28, 4.50 ± 0.19 mm, 11156.87 ± 117.90 pixels, and 2.90 ± 0.18 ng/ml respectively). MiRNA expression analysis was identified during both stages denoting several up and downregulated miRNA candidates among the studied groups. In conclusion, incorporating melatonin enhanced the efficiency of the superovulation regimen in goats under hot climatic conditions.