Entering politics in the Liberal Party while in law school, Núñez aided in the drafting of Colombia's first Liberal constitution (1853) while a member of Congress. He later served in the cabinets of several presidents during the long period of Liberal control of Colombia.

In 1863 Núñez left Colombia for Europe, where he studied other forms of government and came into contact with political thinkers; as a result, he abandoned many of his radical ideas. Returning to Colombia in 1875, Núñez failed in the following year to win the presidency because the Radicals refused to support him. In 1880, with the support of moderates from both the Liberal and the Conservative parties, he won his first term (1880–82) as president. A rebellion of Radicals and Liberals in 1884 forced him further into an alliance with the Conservatives to win election to his second term (1884–86). The constitution of 1886 solidified his regime and inaugurated 50 years of Conservative dominance. Núñez then instituted a series of reforms called the Regeneration, which replaced the supremacy of the various states with a centralized government and restored the power of the Roman Catholic church.

Regarded as the leading intellectual figure in Colombia, Núñez wrote on politics and economic policy and composed volumes of poetry. His regime was often administered by deputies in Bogotá while he ruled from his plantation, where he died.