Inhabited by the native Charrúa people, the site's strategic location on the Salado River made it of interest to Spanish Viceroy Juan José de Vértiz y Salcedo, who established an outpost there in the 1790s as part of a line of defense against raids by displaced natives. The location became known as El Potroso.
El Potroso was reinforced by a fort by way of an 1826 decree by President Bernardino Rivadavia, and on December 27, 1827, the citadel was established under the command of a veteran of the Argentine War of Independence, Bernardino Escribano, as Fuerte de la Federación. The advent of Buenos Aires Province Governor Juan Manuel de Rosas led to Escribano's 1829 destitution as commander; though the intervention of an officer, Isidoro Suárez, averted a bloodbath. Suárez, a veteran of one of last battles of the War for Independence (the Battle of Junín, in Perú), inadvertently gave the failing settlement its new name by his actions: "Junín."
Political conflict and ongoing Indian raids had all but destroyed Junín by the 1830s, however, and this prompted Governor Rosas to send the remaining settlers provisions and to subsidize crop farming in the surrounding, fertile pampas fields. This was followed by a pact with Ranquel Chief Santiago Yanquelén, whereby his people would defend Junín against raids by other tribes. Towards the end of his rule, Rosas appointed José Seguí, among the few Afro Argentines to achieve a commissioned officer's rank, to administer Junín, in 1851. Seguí was an efficient, though repressive commander, and in 1863, he was assassinated at his nearby ranch.
Rosas' 1852 overthrow resulted in the appointment of a justice of the peace, who initially shared governing duties with the military commander. Junín's first general store (Basterreix) opened in 1860, and in 1861, Junín elected its first city council (despite being officially only a fort). The province designated the area as a county in 1864, and with nearly
