The Junín plains were known as the Pampus region, which until the arrival of the Incas was inhabited by a semi-savage, quarrelsome group of people whose rivals were the Tarumas. Meanwhile, the Mantaro Valley was inhabited by the Huancas. Inca Pachacutec conquered all these peoples in 1460, who then became part of the Inca Empire. Huancayo became the region's main roadside resting stop on the Inca Trail.

Wool mills (known in Spanish as obrajes) were set up during the Viceroyalty, when weaving and knitting became a tradition that continues in our days. On September 13, 1825, Simón Bolívar issued a decree creating what is now the Junín Region, to commemorate his victory on the Junín Plains (Junín Battle), the last true cavalry charge in the occidental world where no shot was fired but only saber was used. Great events of national importance occurred during this period: Huancayo hosted the Assembly that issued the 1839 Constitution and on December 3, 1854, Ramón Castilla signed a decree that granted freedom to Afro-Peruvian slaves.