The absence epilepsies are a group of idiopathic generalised epilepsy disorders, which develop during childhood and in about 40% of cases, can persist well into adulthood. Absence epilepsy has been associated with numerous psychiatric, social, and economical co-morbidities along with increased rates of premature mortality. The molecular mechanisms involved in absence seizure development is not well-known. Identifying causal contributors is hindered by the complexity of the disorder, which involves interactions between numerous molecular layers. Thus, a more comprehensive approach, such as multi-omics integration should be considered. The Genetic Absence Epilepsy Rat from Strasbourg (GAERS) strain is a widely-utilised and validated model of absence epilepsy. It recapitulates many phenotypic features observed in humans including early development and continuous persistence of seizures. Male GAERS and non-epileptic control (NEC) rats at three different time points (n = 12/timepoint); 3 weeks, before seizure development, 7 weeks, when seizures begin to develop, and 16 weeks, after seizures have fully developed, were used. The somatosensory cortex (Scx) and thalamus, which are the main brain regions involved in the pathogenesis of absence epilepsy, were analysed by high-resolution mass spectrometry to identify proteins, metabolites and pathways that are significantly altered during absence epilepsy development. In addition, anxiety-like and depressive-like behaviours were tested for in the 7- and 16-week groups followed by EEG electrode implantation and seven days of EEG recordings. To identify dysregulated molecules, proteomics and metabolomics single-omics analyses were conducted, followed by multi-omics integration. Overall, 13 proteins and 4 metabolites were identified in common at all time points and between the brain regions for single-omics analysis. From these, three proteins and three metabolites were identified among the top five dysregulated molecules in both single-omics and multi-omics analyses in the GAERS model. Of significant interest was the dysregulation of the Nit2 enzyme and α-ketoglutaramic acid, both of which are involved in the glutamate metabolism. Nit2 is responsible for the conversion of α-ketoglutaramic acid to 2-oxoglutarate which is in turn converted into glutamate; a neurotransmitter strongly associated with epilepsy. The aberrant expression of these two molecules, even at 3 weeks, indicate that there may be perturbations in neuronal signalling pathways even before seizure develop. Overall, our results suggest that multi-omics integration may be a robust method to use for the identification of potential disease-associated molecules and pathways. Further targeted analysis is required to validate our findings and identify the mechanisms of action for the molecules of interest.