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The first historically recorded contact of the Yawalapiti with non-Indians occured in 1887, when they were visited by the Karl von den Steinen expedition. At that time, they were located on the upper course of the Tuatuari River, in a region situated among lakes and swamps identified by the Yawalapiti as the site of many of their villages. The German ethnologist was impressed with the poverty of these Indians, who hardly had any food to offer to the visitors; the Yawalapiti identify this period as the beginning of their decline as a group, which would culminate in the dissolution of the village in the 1930s. Von den Steinen mentions two Yawalapiti chiefs, Mapukayaka and Moritona (possibly Aritana), names which are still present today in the genealogy of these people, who are able to trace their ascendence to these same contemporaries of von den Steinen.

The Yawalapiti relate how they left the "village of the tucum palms", near the juncture of the Kuluene and Batovi rivers, due to the attacks of the Manitsawá " or, several say, the Trumai " who decimated a great many of them. Tatîwãlu, chief of this village and a very distant historical ancestor of the Yawalapiti, died there. His brother Waripirá and his "cross-cousin" (italuñiri) Yanumaka came up the Kuluene, leading the remaining Yawalapiti. At the mouth of the Tuatuari, there was a division of the group: Yanumaka went on up the Tuatuari and Waripirá went to the headwaters of the Kuluene. Yanumaka’s group settled in Yakunipi, the first village of the present-day Yawalapiti.

Due to their population growth, the Yawalapiti of Yakunipi built other villages in the region known as Puía ("Lake"), a triangle of highlands between lakes and groves of buriti palms fed by a branch of the Twatwarí. The largest village there was Ukú-píti ("village of the arrows"), an ancient Mehinako site, abandoned by them due to spirits who infested the lakes and stole children.

In the mid-1940s, after having occupied the site of Palusáya-píti (previously associated with the Mehinako), the Yawalapiti suffered a serious crisis, which led to a temporary dispersion of their population among the Kuikuro, Mehinako and Kamaiurá villages. At the time of the arrival of the Villas Boas brothers in the region, the Yawalapiti had rebuilt their villages, re-organizing themselves as a group. Between 1948 and 1950, they re-organized on the ancient site of the lakes (Puía), from whence they left (at the suggestion of the Villas Bôas) at the beginning of the 1960s, then moving to Emakapúku, near the Leonardo Post. Presently in the village, besides the "original" Yawalapiti nucleus, there are Kamaiurá, Kuikuro, Kalapalo, Wauja and Mehinako Indians.