Growing evidence from human and animal studies has shown adverse consequences of maternal usage of antidepressants in their newborn babies. To study the effects of early antidepressant exposure on motor function later in life, we treated neonatal rat pups with fluoxetine (FLX), a selective serotonin reuptake inhibitor (SSRI)-type antidepressant, from the day of birth to postnatal day 4 and examined motor performance during adolescence. FLX-treated rats had reduced locomotor activities in an open field and poorer motor performance on an accelerating rotarod compared to the control group of saline-treated animals. Nevertheless, the poorer motor performance largely improved after repetitive practices. To elucidate the structural alterations in the motor system, we examined the structure of neurons in motor-related brain regions. The shape, density and soma size of cerebellar Purkinje cells were comparable in the two groups, however, density of dendritic spine in medial spiny neurons of striatum and layer 5 pyramidal neurons in the primary motor cortex (M1) were reduced in FLX-rats. Furthermore, the basilar dendrites in M1 layer 5 neurons had reduced dendritic complexity than those of the control animals. The impaired dendritic structure in striatal and cortical neurons in FLX-treated rats might account for their poorer motor performances. Together, the structure and function of the motor system are affected by early FLX exposure, the long-term effects of early exposure to SSRI-type antidepressants should be concerned.