This work explored the differences in the fatty acid profile and physico-chemical composition of ghee prepared from the milk of different camel breeds using gas chromatography-mass spectrometry and Fourier transform infrared spectroscopy techniques. Bikaneri ghee was observed to contain 11 individual fatty acids. Chemometric analysis identified the breed-specific differences among various groups. The higher concentration of medium-and long-chain fatty acids along with fatty acid indices (n-3/n-6 ratio, Atherogenic index and Thrombogenic index) in Kachchi ghee established its superiority in terms of nutritional values. Correlation network indicated the strong interdependence of different fatty acids with similar physiological and molecular characteristics, while positions of transmittance peaks confirmed significant differences in the fatty acids.