It was the aim of this field study to evaluate two different protocols of ovulation synchronization for the treatment of ovarian cysts and their effect on reproductive performance in dairy cows. In addition, factors with a possible influence on treatment success and pregnancy outcome as well as costs per pregnancy were analysed. The study was performed with 130 German Holsteins with ovarian cysts diagnosed on days 55 to 60 postpartum. Cows belonging to group 1 (n = 65) received a modified ovsynch protocol [day 0: 0.15 mg cloprostenol (PGF) + 0.02 mg buserelin acetate (GnRH); day 14: PGF; day 16: GnRH]. Group 2 (n = 65) was treated with the conventional ovsynch protocol (day 0: GnRH; day 7: PGF; day 9: GnRH). Timed artificial insemination was performed 20 to 24 h later. Cows without ovarian cysts served as controls. Treatment success (disappearance of the ovarian cyst) after the first ovsynch cycle was higher in group 1 (66.2%) than in group 2 (23.1%, p < 0.05). Reproductive measures in group 1 were comparable with those of the control group and, compared with group 2, were conspicuously better (66.2%, 76.9%, 83.1%, 59.5% vs. 40.0%, 50.7%, 60.0%, 27.5% for cumulative pregnancy rate after treatment cycle 1 to 3 and second service conception rate, respectively, p < 0.05). Overconditioned cows and cows with larger ovarian cysts showed a diminished treatment and pregnancy success. In group 1, costs per pregnancy were only slightly higher than in the control group (group 1: €352.44, group 2: €484.59, control group: €333.77). In conclusion, our results suggest that ovsynch protocols can be used in the treatment of ovarian cysts. The modified ovsynch protocol led to a better cure rate as well as a better reproductive performance, and was economically beneficial compared with a conventional ovsynch protocol.