The tradition of burying horses in Lithuania lasted from the Early Roman period until the late 14th C AD. It was the longest-lasting custom in Europe, which has left about 2000 known horse burials. This paper publishes the osteometric data and age of horses found in Lithuanian cemeteries and castles of the 3rd–14th C AD, over 200 individuals in total. These are the remains of all the horses still stored in Lithuanian institutions. The paper discusses the dynamics of horse body size in order to test previously suggested hypotheses regarding the relationship between large horse body size and its military use, possibly non-local breed, and high social status of the owner. Moreover, we are publishing the AMS 14C dates of 13 horses previously assigned to the Migration period. The research results corrected the existing chronology. The abundant data also allowed an assessment of the development of the size and age of the horses in Lithuania between the 3rd and 14th C AD. Osteometric analyses have shown that Late Roman–post-Migration-period horses were unusually large compared to the Viking and medieval horses in Lithuania. Meanwhile, we suggest that the semi-slender-legged 118–125-cm-tall horse, which predominated in the Viking period, is the most consistent with the local horse type. In general, the horses in Lithuania in the 3rd–11th C AD were small compared to those in Central and Western Europe or Scandinavia. More significant changes can be observed in the Middle Ages. In the 12–14th C AD, there was a much greater variety of horses and the expansion of taller (140–150 cm) individuals. However, the continued abundance of small horses in the medieval times, found buried with saddles and other equipment, allows one to renew the debate on the formation of the cavalry, the tactics of combat, and the social composition of horsemen in Lithuania.