Objective: This study aimed to compare aneuploidy rates and clinical outcomes between trophectoderm biopsy at fresh blastocyst (biopsy-fresh) followed by vitrification and biopsy at vitrified-warmed blastocyst (biopsy-vitri) followed by next day transfer (without re-vitrification). Methods: This retrospective study included 844 patients undergoing 844 cycles conducted from August 2019 to December 2023. Preimplantation genetic testing for aneuploidy (PGT-A) was performed via trophectoderm biopsy using array comparative genomic hybridization or next-generation sequencing for comprehensive 24-chromosome screening. Patients were divided into two groups based on the blastocyst status at the time of biopsy: the biopsy-fresh group (531 patients) and the biopsy-vitri group (313 patients). Results: The clinical pregnancy rate was significantly higher in the biopsy-fresh group compared to the biopsy-vitri group (58.7% vs. 45.6%; odds ratio [OR], 1.695; 95% confidence interval [CI], 1.215 to 2.364; p=0.002). Furthermore, the biopsy-fresh group showed higher implantation rates (45.6% vs. 32.1%; OR, 1.767; 95% CI, 1.274 to 2.451; p=0.002), ongoing pregnancy or live birth rates per cycle (48.0% vs. 35.8%; OR, 1.652; 95% CI, 1.177 to 2.319; p=0.004), and rates of good-quality blastocysts (57.1% vs. 32.1%, p<0.001) compared with the biopsy-vitri group. Miscarriage rates did not differ significantly between the groups (18.2% vs. 21.4%; OR, 0.818; 95% CI, 0.457 to 1.465; p=0.501). Conclusion Biopsy at fresh blastocyst demonstrated superior clinical outcomes compared with biopsy at vitrified-warmed blastocyst, likely due to better embryo quality. Both biopsy at fresh blastocyst and vitrified-warmed blastocyst remain viable options for PGT-A, with biopsy at vitrified-warmed blastocyst serving as a practical alternative. Embryo quality and euploid status continue to be critical considerations for embryo transfer selection.