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Objective: To compare the clinical outcomes and cost‐effectiveness of progestin‐primed ovarian stimulation (PPOS) and the gonadotropin‐releasing hormone‐antagonist (GnRH‐A) protocol in fertility preservation (FP) in cancer patients. The stimulation option when patients were in the luteal phase was also explored. Methods: This retrospective study analyzed clinical data from 163 patients who underwent FP. The number of retrieved oocytes and vitrified oocytes/embryos, total dose of gonadotropin, duration of stimulation, number of injections, and cost were compared among the PPOS, GnRH‐A, and luteal phase stimulation (LPS) groups. Results: No significant differences were noted in the numbers of retrieved oocytes and vitrified oocytes/embryos among the three groups. In the multiple regression model, age (P = 0.02) and antral follicle count (AFC) (P < 0.001), but not the controlled ovarian stimulation (COS) protocols (P = 0.586), were associated with the number of retrieved oocytes. The number of injections and the cost were all significantly lower in the PPOS and LPS groups than in the GnRH‐A group(P < 0.001). Conclusion: PPOS had similar clinical results but was superior medically and economically to GnRH‐A. For patients in the luteal phase, LPS was an optional protocol with similar outcomes and costs to PPOS. Synopsis: PPOS protocols had similar clinical but superior medico‐economic to GnRH‐A. LPS was an optional protocol with similar outcomes and costs as PPOS. [ABSTRACT FROM AUTHOR]