Changes in gene expression in carps’ brains over time following acute stressors has not been studied in detail so far. Consequently, a stress trial with juvenile common carp was conducted to investigate transcriptomic differences in four brain parts in response to acute negative stressors and feed reward, focusing on appetite-related genes, serotonergic and dopaminergic pathways, and other involved systems, at 30, 60, and 90 min after treatments. The treatments showed pronounced effects on the gene expression patterns across brain parts compared to control fish. Notably, npy expression increased in the telencephalon following negative stressors and feed reward, suggesting a stress-coping mechanism by promoting food intake. Unlike zebrafish, cart expression in carp showed varying responses, indicating species-specific regulation of appetite and stress. Serotonergic and dopaminergic pathways were also affected, with alterations in the respective receptors’ expression, confirming their roles in stress and reward processing. Additionally, this study highlights the involvement of the opioid- and gamma-aminobutyric acid systems in stress and feeding regulation across brain parts. Furthermore, principal component analyses revealed that neurotransmitter levels in the different brain parts contribute to the explained variance. These findings deepen our understanding of how different fish species react to acute stress and rewards.