Milk oligosaccharides are believed to have beneficial biological properties. Caprine milk has a relatively high concentration of oligosaccharides in comparison with other ruminant milks and has the oligosaccharide profile closest to that of human milk. The first stage in recovering oligosaccharides from caprine milk whey, a by-product of cheese making, was accomplished by ultrafiltration to remove proteins and fat globules, leaving more than 97% of the initial carbohydrates, mainly lactose, in the permeate. The ultrafiltered permeate was further processed using a 1 kDa ‘tight’ ultrafiltration membrane, which retained less than 7% of the remaining lactose. The final retentate was fractionated by preparative scale molecular size exclusion chromatography to yield 28 fractions; oligosaccharide-rich fractions that were suitable for functionality and gut health promotion testing were detected between fractions 9/10 to 16/17. All fractions were evaluated for their oligosaccharide and carbohydrate profiles using three complementary analytical methods.