Cow milk is the most common dairy milk and has been extensively researched for its functional, technological and nutritional properties for a wide range of products. One such product category is infant formula, which is the most suitable alternative to feed infants, when breastfeeding is not possible. Most infant formulas are based on cow milk protein ingredients. For several reasons, consumers now seek alternatives such as goat milk, which has increasingly been used to manufacture infant, follow-on and young child formulas over the last 30 years. While similar in many aspects, compositional and functional differences exist between cow and goat milk. This offers the opportunity to explore different formulations or manufacturing options for formulas based on goat milk. The use of whole goat milk as the only source of proteins in formulas allows levels of milk fat, short and medium chain fatty acids, -2 palmitic acid, and milk fat globule membrane (MFGM) to be maximised. These features improve the composition and microstructure of whole goat milk-based infant formula, providing similarities to the complex human milk fat globules, and have been shown to benefit digestion, and cognitive and immune development. Recent research indicates a role for milk fat and MFGM on digestive health, the gut-brain axis and the gut-skin axis. This review highlights the lipid composition of whole goat milk-based infant formula and its potential for infant nutrition to support healthy digestion, brain development and immunity. Further work is warranted on the role of these components in allergy development and the advantages of goat milk fat and MFGM for infant nutrition and health.