Congenital viral infections are believed to damage the developing neonatal brain. However, whether neonates exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) show manifestations of such damage remains unclear. For neurodevelopment evaluation, general movement assessments have been shown to be effective in identifying early indicators of neurological dysfunction, including the absence of fidgety movements. This study compared the early motor repertoire by general movement assessment at three to five months of age in neonates who were or were not prenatally exposed to SARS-CoV-2 to determine whether infants prenatally exposed to SARS-CoV-2 are at risk of developing neurological disorders. Fifty-six infants, including 28 in the exposed group of mothers without vaccination who had no need for intensive care and likely had SARS-CoV-2 infection close to the time of pregnancy resolution and 28 infants in the nonexposed group, were videotaped to compare their detailed early motor repertoires, in which a motor optimality score-revised (MOS-R) was calculated using Prechtl’s method by using the chi-square or Mann–Whitney U tests. In the exposed group, 3 (11%) infants showed the absence of fidgety movements with a total MOS-R<14 points, and 3 (11%) other infants showed abnormal fidgety movements. Between groups, atypical body symmetry (p = 0.009) and MOS-R values were significantly lower (Z = -3.08, p = 0.002), with a large size effect (Cohen’s d = 0.97). The consequences of this new virus go beyond the health of the pregnant mother, and these consequences in some of the infants in the exposed group are likely not transitory because of the absence of fidgety movements between 3–5 months; thus, these babies are at increased risk of developing a serious neurological disorder.