ABSTRACT Cystic ovarian disease is one of the leading causes of infertility in dairy cows. In this experimental field study, the comparative efficacy of the −3hCG/Ovsynch protocol (pre‐treatment with hCG before Ovsynch) was investigated alongside the Ovsynch and the progestagen‐based Ovsynch protocol. A total of 45 dairy cows with follicular cyst (FC) were enrolled in the study. The cows were randomly divided into three equal groups: in the first group, the Ovsynch‐48 protocol (Day 0 GnRH, Day 7 PGF 2α , Day 9 GnRH and fixed‐time artificial insemination (FTAI) 16–20 h later); in the second group, the CIDR‐synch protocol (Day 0 GnRH and the insertion of CIDR into the vagina for 7 days, Day 7 PGF 2α , Day 9 GnRH and FTAI 16–20 h later); and in the third group, the −3hCG/Ovsynch protocol (3000 IU hCG pre‐treatment before initiation of the Ovsynch‐48 protocol) were applied. Blood samples were collected on Day −3, 0, 3 and 7, and serum progesterone levels were measured. Transrectal sonography of the ovaries was performed on Day −3, 0, 3 and 7 for ovarian dynamics (follicular development, presence of FC, measurement of diameter and wall thickness of FC) throughout the protocols. Cows were fixed‐time artificially inseminated. On Day 13 (3 days after FTAI) and Day 45 (pregnancy diagnosis), ovarian ultrasonography was also performed to evaluate the cystic persistence (PC). hCG pre‐treatment was found to be ineffective on follicular development in the early period of the −3hCG/Ovsynch protocol, but it significantly increased the diameter of the dominant follicle on Day 3 when compared to the Ovsynch and CIDR‐synch protocols. The lifespan of the corpus luteum in the −3hCG/Ovsynch group was longer (> 4 days) than in the other protocols (< 4 days). Following the Ovsynch, CIDR‐synch and −3hCG/Ovsynch protocols, the PC rates were found to be 54.5% (6/11), 45.4% (5/11) and 27.2% (3/11) on Day 13, and 27.2% (3/11), 27.2% (3/11) and 9.1% (1/11) on Day 45, respectively. Conception rates were found in Ovsynch (6/15), CIDR‐synch (8/14) and −3hCG/Ovsynch (8/15) protocols as 40%, 57.1% and 53.3%, respectively. According to the findings, it was concluded that the −3hCG/Ovsynch protocol may be more effective than the Ovsynch protocol in the treatment of cows with FCs, can be used as an alternative to the CIDR‐synch protocol and can be preferred especially in cows with uterine infection detected early in the postpartum period and in cases where the use of exogenous progesterone is contraindicated.