Kisspeptins are potent secretagogues of gonadotrophin-releasing hormone, playing a key role in puberty onset. These peptides are produced by distinct neuronal populations of the hypothalamus located in the rostral periventricular area of the third ventricle (RP3V) and arcuate nucleus (ARC). The present immunohistochemical study aimed to determine the spatiotemporal onset of kisspeptin-immunoreactivity (-IR) in the neonatal hypothalamus of male and female rats and to evaluate changes in kisspeptin-IR around puberty. Kisspeptin-IR cells and fibres could be detected from the day of birth in the ARC of both males and females. At this stage, only females displayed some kisspeptin-IR fibres in the RP3V. From postnatal day 7 to adulthood, males displayed lower levels of kisspeptin-IR than females in both regions. During infancy, kisspeptin-IR fibre density in the female decreased in the ARC, whereas it increased in the RP3V. A sex-independent decline in RP3V kisspeptin-IR fibre density was observed in the juvenile, followed by a peripubertal increase in RP3V and ARC kisspeptin-IR. These peripubertal increases in kisspeptin-IR occurred at different timings dependent on sex and region. In females specifically, the increase in kisspeptin-IR fibre density occurred first in the ARC and later in the RP3V under constant levels of circulating oestradiol. In conclusion, the present study highlights the expression of hypothalamic kisspeptins soon after birth, as well as the neonatal establishment of a strong and persisting sex difference in ARC kisspeptin-IR in rats. Moreover, a female-specific desynchronisation of the ARC and RP3V was observed with respect to the increase in kisspeptin-IR fibre density around puberty, which was not related to peripubertal variations in circulating oestradiol.