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Background: To analyze population‐based trends in the prenatal diagnosis of sex chromosome aneuploidy (SCA) since the availability of non‐invasive prenatal testing (NIPT). Methods: Retrospective state‐wide data for all prenatal diagnoses performed <25 weeks gestation from 2005 to 2020 in Victoria, Australia. Non‐invasive prenatal testing became locally available from 2012. The prenatal diagnosis rates of SCA as proportions of all prenatal diagnostic tests and all births were calculated. Statistical significance was assessed with the χ2 test for trend, with p < 0.05 considered significant. Results: 46,518 amniocentesis and chorionic villus sampling were performed during the study period, detecting 617 SCAs. There was a significant increase in the rate of prenatal SCAs from 5.8 per 10,000 births in 2005 to 8.7 per 10,000 births in 2020 (p < 0.0001). This increase was predominantly due to 47,XXY cases, 91% of which were ascertained via positive NIPT for this condition in 2020. The prenatal diagnosis rate of 47,XXY significantly increased from 0.8 per 10,000 births in 2005 to 4.3 per 10,000 births in 2020 (p < 0.0001). Conclusion: Screening for SCAs using NIPT has directly led to an increase in their prenatal diagnosis on a population‐wide basis, especially 47,XXY. This has implications for clinician education, genetic counselling, and pediatric services. Key points: What is already known about this topic? Noninvasive prenatal testing for fetal aneuploidy has created new opportunities for the identification of sex chromosome conditions without an ultrasound phenotype. What does this study add? This is the first population‐based data demonstrating the significant rise in prenatal diagnosis of sex chromosome conditions on amniocentesis and chorionic villus sampling, predominantly driven by increases in the prenatal diagnosis of 47,XXY.The prenatal diagnosis rate of 47,XXY has increased from one in 12,500 births to one in 2300.This five‐fold increase in the prenatal diagnosis of 47,XXY has significant clinical implications for health professional education and postnatal management. [ABSTRACT FROM AUTHOR]