Background: Hypertension, a major risk factor for cardiovascular diseases, lacks obvious clinical signs, necessitating new biomarkers for early detection. This study explored plasma and urinary metabolic profiles of 16-week-old spontaneously hypertensive rats (SHR) to identify metabolomic profiles associated with hypertensive characteristics for early diagnosis. Methods: Plasma and 24-hour urine samples from 10 SHR and 10 normotensive Wistar-Kyoto rats were analyzed using high-performance liquid chromatography quadrupole time of flight coupled to mass spectroscopy. Multivariate statistical analysis and mummichog pathway enrichment analysis were performed. Results: Sixteen differential metabolites in plasma and 13 in urine were identified in SHR compared to normotensive rats. Differences in microbiota-derived metabolites suggested gut microbiota changes associated with hypertension. The mummichog algorithm revealed altered metabolism of steroid hormones, bile acids, and purines in hypertensive rats. Conclusions: This study highlights metabolomics as a tool for identifying biomarkers in early hypertension detection. The findings suggest hypertension is associated with alterations in steroid hormone, bile acid, and purine metabolism, as well as microbiota-derived metabolites. These results contribute to understanding hypertension pathogenesis and open avenues for future human research, potentially enabling earlier and more accurate diagnoses to prevent complications.