Purpose <p>To assess the effectiveness of personalized embryo transfer (pET) in enhancing intrauterine pregnancy rates in women with polycystic ovary syndrome (PCOS) without recurrent implantation failure (RIF).</p> Methods <p>This single-center, open-label, randomized controlled trial was conducted at a university-affiliated assisted reproductive medical center between October 2022 and May 2024. Eligible participants were randomly assigned to either the pET arm guided by the RNA-seq-based endometrial receptivity test (rsERT) or the regular frozen embryo transfer (FET) arm. Clinical outcomes from the first embryo transfer cycles following the tests were tracked and compared between the groups.</p> Results <p>A total of 121 patients were included and randomly assigned to either the FET arm (<i>n</i> = 60) or the pET arm (<i>n</i> = 61). Intention-to-treat analyses revealed no significant differences between the FET group and the pET group in terms of intrauterine pregnancy rate (61.2% vs. 60.0%, difference, − 1.2% [95% CI, − 20.2 to 17.9%], <i>p</i> = 0.901), embryo implantation rate (54.7% vs. 50.7%, difference, − 4.0% [95% CI, − 20.5 to 12.8%], <i>p</i> = 0.643), early miscarriage rate (3.3% vs. 6.7%, difference, 3.3% [95% CI, − 11.1 to 18.7%], <i>p</i> = 1.000), and ongoing pregnancy rate (59.2% vs. 56.0%, difference, − 3.2% [95% CI, − 22.3 to 16.2%], <i>p</i> = 0.749). Subgroup analyses of intrauterine pregnancy rates revealed no statistically significant differences between the groups, regardless of the analysis method used.</p> Conclusions <p>Current evidence does not support the routine use of rsERT for personalized embryo transfer in PCOS patients without RIF. Further large-scale, well-designed clinical trials are needed.</p> Trial registration <p>The trial was registered on the Chinese Clinical Trial Registry (registration no. ChiCTR2200064131, prospectively registered). Trial registration date: 2022–09-27.</p>