This study evaluated which endometrial preparation protocol in frozen embryo transfer (FET) cycles provides the best results for polycystic ovarian syndrome (PCOS) patients and the general population. This retrospective study of 634 FET cycles was conducted 2016–2018. Cycles were divided into Group A: Artificial endometrial preparations for FET (aFET; n = 348), Group B: Ovulatory cycle (n = 286) to compare two methods of endometrial preparation for FET. Artificial endometrial preparation with exogenous estrogen and progesterone versus natural ovulation cycles, modified natural cycles using hCG for the final triggering and letrozole-induced ovulation with hCG. Anovulatory patients were analyzed separately. Anovulatory PCOS patients had significantly higher pregnancy rates with letrozole treatment compared with aFET cycles (44% vs. 22.5%; p = 0.044). For the entire cohort, ovulatory cycles and aFET were similar in terms of patient characteristics, demographics, infertility causes, treatment protocols and number of embryos transferred. Although the mean ESHRE score of the transferred embryos was higher in the aFET group, we found higher clinical pregnancy rate in the ovulatory cycle FET (41.3% vs. 27.3%, p < 0.0001). A better pregnancy rate was found after ovulatory cycle FET. In the ovulatory cycles, the outcome of letrozole-induced and non-induced cycles were comparable. PCOS patients, as well as the general population, may benefit from ovulation induced FET cycles, with significantly better outcomes in FET in ovulatory cycles.