A 41-year-old woman with severe autoimmune disease faced repeated failures in non-invasive prenatal testing (NIPT) due to low fetal DNA fractions, prompting her to ultimately proceed with an amniocentesis. After treatment with steroids and intravenous immunoglobulin (IVIG), a subsequent NIPT yielded a low-risk result for trisomies, although another sample showed high variance in DNA counts. The case highlights caution in counseling women with severe autoimmune conditions regarding NIPT due to potential complications and low success rates.