Understanding the metabolic profile within the follicular microenvironment is crucial for optimizing reproductive efficiency in camels. In this study, we examined the metabolomic profile of camel follicular fluid (FF) during the breeding (n = 10) and non-breeding seasons (n = 10). Gas chromatography-mass spectrometry (GC-MS) was utilized to describe the metabolites present in follicular fluid samples. The results found considerable differences in the metabolomics profiles between the breeding and non-breeding seasons. Hexadecenoic acid, galactose and glucose levels were significantly (P <
0.05) higher in camel FF during the breeding season, while 9-octadecenamide, oleonitrile, glycine, octadecanamide, cholesterol, and propanoic acid were higher (P <
0.05) in FF during the non-breeding season. Multivariante analyses pointed to those 9 metabolites, and univariate analysis showed hexadecenoic acid, galactose, glucose, and oleanitril were the most significant ones in camel follicular fluid collected during both breeding and non-breeding seasons. The univariate and multivariate analyses showed an increase in the levels of hexadecanoic acid, galactose, glucose, and a depletion in the level of oleanitrile in the breeding season compared to the non-breeding season. The ROC curve and statistical analysis showed that hexadecanoic acid, galactose, and oleanitril with AUC = 1 were promising to be seasonal biomarkers of fertility in female camels. In conclusion, the metabolomic analysis of camel FF reveals distinct changes in metabolite levels between breeding and non-breeding seasons, reflecting adaptive metabolic responses to support reproductive processes. These results offer valuable insights into the reproductive physiology of camels and offer practical implications for potential biomarkers and assessing the reproductive status in camels, which can be utilized in reproductive management and conservation efforts in these valuable animal species.