The beginning of agriculture marks major changes in food acquisition technology in human history. In the southern Caucasus, agricultural villages emerged around 6000 cal. BC, 2000 to 3000 years later than in the Fertile Crescent despite their geographical closeness to each other. This study aims to provide isotopic evidence indicative of animal herding strategies in the early farming communities in the southern Caucasus. To analyze intra-individual sequential carbon and oxygen isotope variations, we used tooth enamel of five goats, four sheep, and three cattle from the Neolithic settlements, Göytepe and Hacı Elamxanlı Tepe (Azerbaijan). The analyses also included reference samples of modern domestic goat and sheep that are known to have grazed in the vicinity of the sites. As a result, the sequential carbon and oxygen isotope variations of the modern goat and sheep samples showed large amplitude and a synchronous pattern during the whole enamel maturation period. The same pattern was observed in some of the Neolithic goat and sheep samples, suggesting they may have grazed in the vicinity of the lowland site throughout the year. Other Neolithic goat and cattle samples exhibited relatively small amplitudes and inverse cyclical variation patterns. While these patterns may have been caused by multiple factors, such as drinking water and food/fodder, vertical transhumance has also been proposed for the similar isotope patterns. Despite the difficulty in specifying exact causes for the observed isotopic patterns, their diversity within/among the species implies multiple pastoral strategies that may have had adaptive advantages in new agricultural frontiers in the southern Caucasus.