Juárez was born in the small village of San Pablo Guelatao, Oaxaca on March 21, 1806, located in the mountain range now known as the "Sierra Juárez." His parents, Marcelino Juárez and Brígida García, were peasants who died when he was three years old. He described his parents as "indios de la raza primitiva del país," that is, "Indians of the original race of the country." He worked in the corn fields and as a shepherd until the age of 12, when he walked to the city of Oaxaca to attend school. At the time, he was illiterate and could not speak Spanish, only Zapotec. In the city, where his sister worked as a cook, he took a job as a domestic servant for Antonio Maza. A lay Franciscan, Antonio Salanueva, was impressed with young Benito's intelligence and thirst for learning, and arranged for his placement at the city's seminary. He studied there but decided to pursue law rather than the priesthood. He graduated from the seminary in 1827 and went on to gain a degree in law. In 1843 Benito married Margarita Maza.

Juárez became a lawyer in 1834 and a judge in 1841. He was governor of the state of Oaxaca from 1847 to 1852; in 1853, he went into exile because of his objections to the corrupt military dictatorship of Antonio López de Santa Anna. He spent his exile in New Orleans, Louisiana, working in a cigar factory. In 1854 he helped draft the Plan of Ayutla as the basis for a liberal revolution in Mexico. Faced with growing opposition, Santa Anna resigned in 1855 and Juárez returned to Mexico. The winning party, the liberales (liberals) formed a provisional government under General Juan Álvarez, inaugurating the period known as La Reforma. The Reform laws sponsored by the puro (pure) wing of the Liberal Party curtailed the power of the Catholic Church and the military, while trying to create a modern civil society and capitalist economy based on the U.S. model. The Ley Juárez (Juárez's Law) of 1855, for example, abolished special clerical and military privileges, and declared all citizens equal before the law. All the efforts ended on the promulgation of the new federalist constitution. Juárez became Chief Justice, under moderado (moderate) president Ignacio Comonfort.

The conservadores (conservatives) led by General Félix Zuloaga, with the backing of the military and the clergy, launched a revolt under the Plan of Tacubaya on December 17, 1857. Comonfort did not want to start a bloody civil war, so made an auto-coup d'état, dissolved the congress and appointed a new cabinet, in which the conservative party would have some influence, assuming in real terms the Tacubaya plan. Juárez, Ignacio Olvera, and many other deputies and ministers were arrested. The rebels wanted the constitution revoked completely and another all-conservative government formed, so they launched another revolt on January 11, 1858, proclaiming Zuloaga as president. Comonfort re-established the congress, freeing all the prisoners and resigned as president. Under the new constitution, the chief justice immediately became interim president until proper elections could be made. Juárez took office in late January 1858. Juárez then led the liberal side in the Mexican War of the Reform, first from Querétaro and later from Veracruz. In 1859, Juárez took the radical step of declaring the confiscation of church properties. In spite of the conservatives' initial military advantage, the liberals drew on support of regionalist forces. They had U.S. help under some terms of the controversial and never approved McLane-Ocampo treaty. This turned the tide in 1860; the liberals recaptured Mexico City in January 1861. Juárez was finally properly elected president in March for another four-year term, under the Constitution of 1857.

Faced with bankruptcy and a war-savaged economy, Juárez declared a moratorium on foreign debt payments. Spain, Great Britain, and France reacted with a joint seizure of the Veracruz customs house in December 1861. Spain and Britain soon withdrew, but the French Emperor Napoleon III used the episode as a pretext to launch the French intervention in Mexico in 1862, with plans to establish a conservative regime. The Mexicans won an initial victory over the French at Puebla in 1862, celebrated annually as Cinco de Mayo (May 5). The French advanced again in 1863, forcing Juárez and his elected government to retreat to the north, first to San Luis Potosí, then to the arid northern city of El Paso del Norte, present day Ciudad Juárez, Chihuahua, and finally to the capital of the state, Chihuahua City, where he set up his cabinet and government-in-exile. There he would remain for the next two and one-half years. Meanwhile Maximilian von Habsburg, a younger brother of the Emperor of Austria, was proclaimed Emperor Maximilian I of Mexico on April 10, 1864 with the backing of Napoleon III and a group of Mexican conservatives. Before Juárez fled, Congress granted him an emergency extension of his presidency, which would go into effect in 1865, when his term expired, and last until 1867 when the last of Maximilian's forces were defeated.

In response to the French intervention and the elevation of Maximilian, Juárez sent General Plácido Vega y Daza to the U.S. State of California to gather Mexican American sympathy for Mexico's plight. Maximilian, who personally harbored liberal and Mexican nationalist sympathies, offered Juárez amnesty, and later the post of prime minister, but Juárez refused to accept either a government "imposed by foreigners", or a monarchy. A legitimate Mexican throne had existed long before him, founded by Emperor Augustine I after independence had been achieved in 1821, but was abolished only a year later, during a domestic crisis. With its own civil war over, President Andrew Johnson invoked the Monroe Doctrine to give diplomatic recognition to Juárez' government and supply weapons and funding to the Republican forces. When he could get no support in Congress, he supposedly had the Army "lose" some supplies (including rifles) "near" (across) the border with Mexico. He would not even meet with representatives of Maximilian. Gen. Philip Sheridan wrote in his journal about how he "misplaced" 30,000 muskets close to Mexico. Faced with this and a growing threat from Prussia, the French troops began pulling out of Mexico in late 1866. Mexican conservatism was a spent force and was less than pleased with the liberal Maximilian. In 1867 the last of the Emperor's forces were defeated and Maximilian was sentenced to death by a military court. Despite national and international pleas for amnesty, Juárez refused to commute the sentence, and Maximilian was executed by firing squad on June 19, 1867 at Cerro de las Campanas in Queretaro. His body was returned to Europe for burial. His last words had been, '¡Viva México!'

Juárez was controversially re-elected President in 1867 and 1871, using the office of the presidency to ensure electoral success and suppressing revolts by opponents such as Porfirio Díaz. Benito Juárez died of a heart attack in 1872 while working at his desk in the National Palace in Mexico City. He was succeeded by Sebastián Lerdo de Tejada, his foreign minister.

During the 19th century Mexico was characterized by political, social and economical instability. The balance of power in the American continent moved remarkably to the United States. In 1836 Texas gained its independence from Mexico. Afterwards, Mexico also lost the territory that today constitutes the American states of Arizona, California and New Mexico. Twenty six years later in 1862, Napoleon III, attempted to establish a French colony in Mexico. Mexico was a vulnerable country in the 19th century invaded by two powerful nations; the United States and France. Both nations lent money to Mexico; however, it was not because they were interested in helping the Mexicans, but strictly for economical and political reasons. The United States rooted its support for Juarez in the Monroe Doctrine. They wanted to shield the Western Hemisphere from European influences. This left Juarez as the favored Mexican candidate of the United States government. Juarez would not have defeated the conservatives and Maximilian without some intervention from the United States.

Tomás Mejía (1820-1867), a Mexican general, opposed the Liberal Reform Movement, and was shot along with Maximilian under Juarez’s orders. Afterward, liberals that were in power by that time erased his name from history in order to clean their reputation. Mejía was powerful because of his father who was a cacique, a person who owned massive amounts of land. He fought in the war against the United States in 1846 and 1847. He was an expert in irregular warfare. Mejía and other conservative generals opposed the McLane-Ocampo Treaty of 1859 because it allowed the United States to cross Mexican territory. Mejía perceived the Treaty as a threat towards Catholicism, race, and Mexican customs and traditions. After the Liberals achieved political control, Mejía took refuge in the mountains along with 1500 men. The 7,000 man force sent by Juarez failed to defeat him. Then Juarez offered a 10,000 pesos bounty, saying that Mejia was a threat to national security and stability.