Non-invasive prenatal testing (NIPT) has grown in ubiquity in the last decade and is now endorsed by Society for Maternal Fetal Medicine and American College of Obstetricians and Gynecologists as a screening tool for aneuploidy in all patients. Past studies have demonstrated a tendency among obstetrics patients to focus on the ability of NIPT to predict fetal sex chromosomes; however, data on the experiences of genetic counselors (GCs) counseling on NIPT and fetal sex prediction are limited. This mixed-methods study aimed to explore how GCs counsel about NIPT and fetal sex prediction, as well as the use of gender-inclusive language in this setting. A 36-item survey with multiple choice, Likert scale, and open-ended questions was distributed to GCs who currently offer NIPT to patients. Quantitative data were analyzed using R and qualitative data were manually analyzed and coded via inductive content analysis. A total of 147 individuals completed at least some portion of the survey. A majority of participants (68.5%) reported frequent interchangeable use of the terms ‘sex’ and ‘gender’ by patients. A majority (72.9%) of participants reported that they rarely or never discuss the difference between these terms in sessions (Spearman's rho = 0.17, p = 0.052). Seventy-five respondents (59.5%) indicated that they had taken continuing education courses on inclusive clinical practices for trans and gender-diverse (TGD) patients. Several themes arose from free responses; the most frequently identified themes were the need for thorough pretest counseling that properly describes the scope of NIPT and the challenge of discrepant pretest counseling by other healthcare providers. Results from our research identified challenges and misconceptions GCs face when offering NIPT and various tactics implemented to mitigate these. Our study highlighted the need for the standardization of pretest counseling regarding NIPT, additional guidance from professional organizations, and continuing education focused on gender-inclusive language and clinical practices.