Animal models of depression offer an alternative research-platform to clinical studies where limitations such as incomplete medical histories, patient heterogeneity, and difficulty tracking comorbidities leading to depression can be more easily overcome. In that context the Wistar Kyoto (WKY) rat strain has for many years been used as an endogenous model of depression. Here we want to further explore the depressive-like phenotype of the WKY rats to extend its validity as a preclinical model of depression. For this purpose, 49 microRNAs (miRNAs), which have been linked to the neurotrophic hypothesis of depression were selected and their levels were examined in hippocampus, prefrontal cortex, and blood from the WKY rats. Subsequently, miRNA/target mRNA/protein relationships were explored. Seventeen miRNAs across brain and blood exhibited significant regulation (>30%). Fifteen of 17 miRNAs were upregulated in the WKY rats, when compared to the Wistar Hannover Galas rats. This was coupled with general downregulation of corresponding mRNA targets in both brain regions. We observed decreased mRNA levels in both brain regions, which was coupled with increased miR-103-1 and miR-212 levels (targeting ). While the relationship between mRNA and protein was not entirely linear, we did observe downregulation of TrkB protein in the prefrontal cortex and downregulation of fully mature glycosylated TrkB in both brain regions. This may indicate disruption of the BDNF-TrkB pathway in WKY rats. In conclusion, this study identifies several molecular alterations in brain and blood from the WKY rats and highlights the WKY rat strain as a viable model of depression.