The aim of this study was to evaluate the effect of the freeze-drying process on the preservation of mare’s milk. This was achieved through the characterization of the functional properties of reconstituted freeze-dried mare’s milk. The chemical composition, bulk density, foam capacity, and ability to form emulsions of the atherogenic, thrombogenic, and hypercholesterolemic fatty acid index were investigated. The freeze-drying process did not change the proportion of the milk components in the dry matter. The moisture content of the freeze-dried mare’s milk was 10.3 g/kg and the bulk was below 0.1 g/mL. The foaming capacity was 111.3%; hence, the foaming capacity of the milk was very poor. The oil binding capacity was 2.19 g/g of protein. The freeze-drying process improves the binding degree and retention of oil by milk proteins, but produced foam was unstable, short-lived, and lacked the ability to retain air fractions. The atherogenic index and thrombogenic index values calculated for reconstituted milk were 1.02 and 0.53, respectively. The hypercholesterolemia fatty acid index was 25.01.