Extracellular vesicles (EVs) have been identified in the uterine fluid in different species and pointed as key players in the embryo-maternal dialogue, maternal recognition of pregnancy (MRP) and establishment of pregnancy. However, little is known about the uterine EVs in the mare. Therefore, the present study aimed at characterizing EVs from uterine lavage of cyclic mares by comparing five EVs isolation methods and the combination of them: (1) Ultracentrifugation (UC); (2) Concentration of lavage volume by Centricon ultrafiltration (CE); (3) the use of CE with different washing steps (PBS versus trehalose); (4) Size-exclusion chromatography with iZON-qEV columns to yield high-purity EVs and (5) a combination of the methods with best results based on EVs yield, purity, and protein cargo profiles. Transmission electron microscopy and Western blotting confirmed the isolation of EVs by all methods but with quantitative and qualitative differences. Mass spectrometry provided different protein profiles among methods with marked differences in the number of proteins and protein classes. Our results indicate that the combination of CE/trehalose/iZON/UC is an optimal method to isolate equine uterine EVs with good yield and purity that can be applied in future studies to determine the role of uterine EVs during MRP in the mare.