Disruption of circadian regulation, particularly during the early developmental stages (EDS), can have deleterious, long-lasting effects. Previous studies have shown that melatonin is involved and that susceptibility to chronodisruption in rats is sex-dependent. Our aim was to investigate the effect of chronodisruption via constant light (LL) during EDS on the clock in the suprachiasmatic nucleus (SCN) of male and female mice naturally deficient in melatonin. We used PER2::LUC knock-in mice, which allows monitoring of clock function in organotypic explants ex vivo. First, we showed that the SCN clock parameters did not exhibit any sex differences at fetal (embryonic day 17.5, E17.5) and adult stages. Next, we exposed the mice to LL either during the gestation (group 1), during the postnatal period (group 2), or during the puberty (group 3). In group 1, we compared bioluminescence parameters in the SCN explants at E15.5 and E17.5 between fetuses of control and LL-exposed pregnant dams. Interestingly, we observed that maternal chronodisruption had a greater impact on the SCN of male fetuses. Surprisingly, the effects of LL on the SCN during EDS persisted into adulthood in groups 1 and 2 when it affected the period in a sex-dependent manner and caused phase-advance in both males and females. Our data show that chronodisruption during EDS affects the SCN clock via melatonin-independent pathways and in a sex-dependent manner. The results emphasize the detrimental effects of artificial light during the subjective night for pregnant women and newborns.