Branched‐chain fatty acids (BCFAs) are mostly saturated fatty acids with a methyl branch at the penultimate or antepenultimate position to the CH3 end. Very‐long‐chain BCFAs (C ≥ 20) are uniquely found in surface lipids. Human and California sea lion (Zalophus californianus) are the only two species that possess vernix at birth, and vernix particles carry loads of BCFA to the gut, potentially influencing the establishment of the first microbiota. Horse (Equus caballus) contains high levels of BCFA in its surface lipids, and the current study aims to investigate if BCFA are components of a neonatal foal's gut. Electron ionization tandem mass spectrometry was used to distinguish iso‐ and anteiso‐form of BCFA from straight‐chain fatty acids. Abundant very‐long‐chain iso‐BCFA, mainly even‐numbered iso‐20:0, iso‐22:0, iso‐24:0, and iso‐26:0 were found in horse meconium but not in their manure collected a few months later. There are little differences in BCFA types and concentrations between foal manure and adult manure. Moderate to high levels of very‐long‐chain anteiso‐BCFA were also found. Comparisons of horse meconium BCFA to horse skin cholesterol ester BCFA content and to meconium from human and sea lion suggest its skin derived origin. The study expands our knowledge on the gut nutritional environment of a newborn horse, and further study is needed to establish the relationship between gut BCFA and microbiota composition in the first few hours of life.Practical Applications: Branched‐chain fatty acids (BCFA) are bioactive compounds found in vernix caseosa, the lipid‐laden material covering the surface of a newborn baby. BCFA also reaches high concentrations from the third trimester of gestation until birth. However, the exact functionality and mechanisms of BCFA in the surface and gut of a fetus remain unclear. The current study aims to clarify the lipid conditions in the gut of newborn foals and to identify the associations between BCFA in the gut and on the skin at a critical point when the horse's microbiota establishes itself. The findings of the current study lay a path for studying the physiological functions of BCFA in horse models, potentially accelerating research related to BCFA.