Hormonal products have been developed for fixed-time artificial insemination (FTAI) to improve the efficiency of swine production. Here, we evaluated the effect of an FTAI protocol initiated during different phases of the estrous cycle on follicle development and ovulation in gilts. A total of 36 gilts were equally divided into three groups designated as the luteal (L), follicular (F), and post-ovulation (O) groups and fed with 20 mg of altrenogest for 18 days, followed by intramuscular injection of 1000 IU PMSG at 42 h after withdrawal of altrenogest, and 100 μg of GnRH after an 80-h interval. The L group had the highest number of follicles 4-6 mm in diameter, as well as corpora hemorrhagica. The mRNA expression of caspase-9 in the L group were significantly lower than those in the O and F groups (P < 0.05), while CYP11A1 and VEGF mRNA expression levels were significantly higher (P < 0.05). Moreover, FSHR mRNA levels were significantly higher in the O group than in the L, F, and control groups (P < 0.05). LHCGR and CYP19A1 mRNA levels were the highest in the F group (P < 0.05). Thus, the changes in the expression of genes associated with follicular development, maturation, and ovulation identified in this study indicated that initiation of the FTAI protocol during the luteal phase induced a better environment for follicle development and ovulation in gilts.