Objective: To assess the clinical characteristics, pregnancy courses, and outcomes in fetuses showing normal nuchal translucency (NT) with septations at a crown-rump length (CRL) below 45 mm. Materials and methods: During a 33-month period from July 2019 to March 2022, nine fetuses showing normal NT with septations (CRL: 22.3–43.3 mm) (NNTS group) and six cystic hygromas (CRL: 27.7–42.8 mm) (CH group) were identified at 9⁺¹–11⁺² weeks of gestation. Their clinical characteristics, pregnancy courses, and outcomes were investigated and compared between the groups. Results: There were no significant differences in gestational age at examination, maternal age, parity, CRL, or prevalence of hydrops between NNTS and CH groups. There were significant differences in NT thickness between NNTS [1.66 (mean) ± 0.24 (standard deviation (SD)) mm] and CH [4.6 (mean) ± 0.93 (SD) mm] groups (p = 0.002). Good outcomes were noted in all cases (100%) in the NNTS group, whereas only two cases had healthy fetuses (33.3%) in the CH group (p = 0.004). In the NNTS group, seven fetuses (not determined in two fetuses) had normal ductus venous flow on first-trimester fetal ultrasound scan. Conclusion: Normal NT with septations at CRL below 45 mm may not be an ominous sign, whereas CH at CRL below 45 mm may still be associated with poor fetal outcomes. However, the data and its interpretation in our study should be taken with some degree of caution because of the small number of subjects studied in both groups. Further studies involving a larger sample size of normal NT with septations at CRL below 45 mm would be needed to ascertain whether nuchal septations are a benign or an ominous sign in clinical practice.