Juan Ramírez de Velasco founded the city with the name Todos los Santos de la Nueva Rioja on 20 May 1591, while he was the Governor of the Territories of Tucumán, and in homage to the region of La Rioja in Spain.
Around the time of the Easter celebrations of 1591 approximately 9,000, of the estimated 11,000 indigenous people living in the surrounding area, attacked the stronghold of La Padercitas in La Rioja as a protest to the poor treatment they received from the Spanish settlers. During this time the Spanish settlers looked to San Francisco Solano to re-establish the peace.
La Rioja was always the principal settlement of the province. The only time it was surpassed in population was in the mid-19th century when Chilecito, a small settlement near the Chilean boarder based around the Hacienda Santa Rita, became the largest town in the province. It wasn't until the early 20th century that La Rioja regained the status of being the largest city.
The city was the only settlement of some importance in the territory of the present province, and when an earthquake severely damaged the city in 1894, it had only 8,000 inhabitants. It was not until the 1970s that the population of the city, and of the province, started growing considerably