Artificial Intelligence (AI)-based algorithms are increasingly entering clinical practice, aiding in the assessment of fetal anatomy and biometry. One such tool for evaluating the fetal head and central nervous system structures is SonoCNS™, which delineates appropriate planes for measuring head circumference (HC), biparietal diameter (BPD), occipitofrontal diameter (OFD), transcerebellar diameter (TCD), width of the posterior horn of the lateral ventricle (Vp), and cisterna magna (CM) based on a 3D volume acquired at the level of the fetal head’s thalamic plane. This study aimed to evaluate the intra- and interobserver variability of measurements obtained using this software. The study included 381 patients, 270 in their second trimester of pregnancy (70%) and 111 in the third trimester. Each patient underwent manual biometric measurements of the aforementioned structures and twice using the SonoCNS software. We calculated the intraobserver variability between the manual measurements and the average of the automated measurements, as well as the interobserver variability for automated measurements. We also compared the median examination time for manual and automated measurements. The interclass correlation coefficients (ICC) for interobserver and intraobserver variability for parameters BPD, HC, and OFD ranged from good to excellent reproducibility in the general population and subgroups (> 0.75). CM and Vp measurements, both in the general population and subgroups, fell into the category of moderate (0.5–0.75) and poor reproducibility (< 0.5). TCD measurements showed moderate (> 0.5) to good reproducibility (0.75–0.9), and OFD showed good and excellent reproducibility. The assessment of the biometry of fetal head structures using SonoCNS took an average of 63 s compared to 14 s for manual measurement (p < 0.001). The SonoCNS™ software is characterized by good to excellent reproducibility and repeatability in the measurement of fetal skull biometry (BPD, HC, and OFD), with poorer performance in measurements of intracranial structures (CM, Vp, TCD). Apart from biometric parameters, the software is useful in clinical practice for delineating appropriate planes from the acquired volume of the fetal head and shortening examination time.