There is no archaeological evidence bearing on the prehistory of the Yawalapití. It is thus impossible to determine precisely how long they have lived in the upper Xingu. The region has been occupied by many small Arawakan and Caribbean ethnic groups before settlement by Tupían, Gê, and some isolated groups. The upper Xingu River Basin was not a main migration route but was inhabited by many small ethnic groups. In the past, wars among the groups and raids from the east (especially by the Trumai group) were common. First contact with Westerners was relatively late. Karl von Steinen's first expedition in 1884 discovered unknown groups on the Rio Batoví, and on his second expedition in 1887, navigating the Rio Culiseu, he met the Yawalapití.
The Roncador-Xingu Expedition in 1949, led by the Villas Boas brothers, was the beginning of stabilization for the Yawalapití. The Xingu National Park, founded in 1961 by the Villas Boas brothers, was transferred in 1967 to the Fundação Nacional do Índio (National Indian Foundation, FUNAI), a part of the Ministry of the Interior. Because of the vast forest surrounding the Yawalapití settlement, it is very difficult for tradesmen, settlers, and even missionaries to gain access. The Yawalapití and other groups of the upper Xingu retain their traditional cultural languages, although the influence of Portuguese and Brazilian consumer society is now felt. The Yawalapití live very near the Leonardo Villas Boas Indian Post, which has a small landing strip and radio contact with the headquarters of FUNAI in Brasília, so they are becoming intermediaries between Brazilians and other groups of the upper Xingu.