Depressive illness has been associated with impaired cognitive processes accompanied by reduced neurotrophin levels, especially brain-derived neurotrophic factor (BDNF), and dysfunctions in the hypothalamic-pituitary-adrenal (HPA) axis. In addition, depression is characterized by a decreased functioning of the serotonergic system due to changes in the activity or expression of its receptors including, most significantly, 5-HT1A, 5-HT2A, and 5-HT3 in brain regions that regulate mood, emotions, and memory, such as the prefrontal cortex, hippocampus, and amygdala. In this regard, rats treated with clomipramine (CMI) in the neonatal stage show depression-like behaviors that persist into adulthood; hence, this constitutes an adequate model of depression for exploring various molecular aspects associated with the etiology of this disorder. This, study, then, was designed to analyze the long-term effects of early postnatal exposure to CMI on the expression of 5-HT1A, 5-HT2A, and 5-HT3 receptors, as well as BDNF and GR in the following brain regions: PFC, amygdala, hippocampus, and hypothalamus, which could be related to alterations in memory and learning, as evaluated using the novel object recognition (NOR) and Morris water maze (MWM). Expression of the 5-HT1A, 5-HT2A, and 5-HT3 receptors, BDNF, and the glucocorticoid receptor (GR) was assessed by RT-qPCR in the four aforementioned brain regions, all of which play important roles in the control of memory and mood. Findings show that neonatal treatment with CMI causes alterations in memory and learning, as indicated by alterations in the results of the MWM and NOR tests. Expression of the 5-HT1A receptor increased in the hippocampus, amygdala, and hypothalamus, but decreased in the PFC, while the 5-HT2A and BDNF receptors decreased their expression in the PFC, amygdala, and hippocampus. There was no change in the expression of the 5-HT3 receptor. In addition, expression of GR in the hippocampus and PFC was low, but increased in the hypothalamus. Taken together, these data show that neonatal CMI treatment produces permanent molecular changes in brain regions related to learning and memory that could contribute to explaining the behavioral alterations observed in this model.