There is evidence that antidepressant drug treatment during a critical period of postnatal development renders mice susceptible to depression- and anxiety-related behaviour in adulthood. The mechanism of how early antidepressant treatment brings about long-term effects in emotional behaviour is not yet understood, but neurotrophins, particularly brain-derived neurotrophic factor (BDNF), have been implicated in this context. We examined the long-term effects of a transient early postnatal fluoxetine treatment on depression- and anxiety-related behaviours as well as gene expression of BDNF and its receptor TrkB in C57BL/6J mice. Treatment with fluoxetine between postnatal days P4 and P21 resulted in a significant loss of body weight and long-lasting behavioural inhibition in adult mice in response to stressful events such as the light-dark or open field tests. Postnatal fluoxetine exposure also decreased behavioural despair in the forced swim test. Both body weight and behavioural alterations were restored by chronic fluoxetine treatment in adulthood. The behavioral alterations were accompanied by changes in hippocampal BDNF mRNA. Specifically, we show that early-life fluoxetine exposure resulted in the long-term upregulation of BDNF expression in adult mice. However, chromatin immunoprecipitation studies did not reveal any changes in the acetylation or trimethylation of histone H3 at the BDNF promoters. Our experiments show that behavioural and molecular changes induced by early postnatal fluoxetine administration are reversed by chronic fluoxetine treatment of adult mice to control levels.