Batista was born in the town of Veguita, located in the municipality of Banes, Cuba, province of Holguín, in 1901, to Belisario Batista Palermo and Carmela Zaldívar González, who had fought in the Cuban War of Independence. He was of Spanish, African, Taíno, and Chinese descent. His mother named him Rubén and gave him her last name, Zaldívar. His father did not want to register him as a Batista. In the registration records of the Banes courthouse, he was legally Rubén Zaldívar until 1939, when, as Fulgencio Batista, he became a presidential candidate and it was discovered that this name did not exist in the birth certificates; he thus had to postpone the presentation of his candidacy and pay 15,000 pesos to the local judge.

Both Batista's parents are believed to have been of mixed race, and one may have had indigenous Caribbean blood. Batista was initially educated at a public school in Banes, and later attended night classes at an American Quaker school. He left home at age 14, after the death of his mother. Coming from a humble background, he earned a living as a laborer in the cane fields, docks, and railroads. He was a tailor, mechanic, charcoal vendor and fruit peddler. In 1921, he traveled to Havana, and in April joined the army as a private. After learning shorthand and typing, Batista left the army in 1923, working briefly as a Teacher of stenography before enlisting in the Guardia Rural (rural police). He transferred back to the army as a corporal, becoming secretary to a regimental colonel. In September 1933, he held the rank of sergeant stenographer and as such acted as the secretary of a group of non-commissioned officers who led a "sergeant's conspiracy" for better conditions and improved prospects of promotion.

Batista married Elisa Godínez y Gómez (1900–1993) on July 10, 1926. They had three children: Mirta Caridad (1927–2010), Elisa Aleida (born 1933), and Fulgencio Rubén Batista Godínez (1933–2007). They divorced in October 1945.

A short-lived five-member presidency, known as the Pentarchy of 1933, was established. The Pentarchy included a representative from each anti-Machado faction. Batista was not a member, but controlled Cuba's armed forces. Within days, the representative for the students and professors of the University of Havana, Ramón Grau San Martín, was made president—and Batista became the Army Chief of Staff, with the rank of colonel, effectively putting him in control of the presidency. The majority of the commissioned officer corps were forced to retire or, some speculate, were killed.

Grau remained President for just over 100 days before Batista, conspiring with the U.S. envoy Sumner Welles, forced him to resign in January 1934. Grau was replaced by Carlos Mendieta, and within five days the U.S. recognized Cuba's new government, which lasted eleven months. Batista then became the strongman behind a succession of puppet Presidents until he was elected President in 1940. After Mendieta, succeeding governments were led by José Barnet (5 months) and Miguel Mariano Gómez (7 months) before Federico Laredo Brú ruled from December 1936 to October 1940.

In a bid to profit from such an environment, Batista established lasting relationships with organized crime, notably with American mobsters Meyer Lansky and Lucky Luciano, and under his rule Havana became known as "the Latin Las Vegas". Batista and Lansky formed a friendship and Business relationship that flourished for a decade. During a stay at the Waldorf-Astoria in New York in the late 1940s, it was mutually agreed that, in return for kickbacks, Batista would give Lansky and the Mafia control of Havana's racetracks and casinos. After World War II, Luciano was paroled from prison on the condition that he permanently return to Sicily. Luciano secretly moved to Cuba, where he worked to resume control over American Mafia operations. Luciano also ran a number of casinos in Cuba with the sanction of Batista, though the American government eventually succeeded in pressuring the Batista government to deport him.

Cuba entered World War II on the side of the Allies on December 8, 1941, declaring war on Japan the day after the attack on Pearl Harbor. On December 11, the Batista government declared war on Germany and Italy. In December 1942, after a friendly visit to Washington, Batista said Latin America would applaud a decision by the United Nations to go to war with Francisco Franco's Spain, calling the regime "fascist".

In 1944, Batista's handpicked successor, Carlos Saladrigas Zayas, was defeated by Grau. In the final months of his presidency, Batista sought to handicap the incoming Grau administration. In a July 17, 1944, dispatch to the U.S. Secretary of State, U.S. Ambassador Spruille Braden wrote:

He later married Marta Fernández Miranda (1923–2006) on November 28, 1945, and they had five children: Jorge Luis (born 1942), Roberto Francisco (born 1947), Carlos Manuel (1950–1969), Fulgencio José (born 1953) and Marta María Batista Fernández (born 1957). He also had an illegitimate daughter, Fermina Lázara Batista Estévez (born 1935).

Lansky became a prominent figure in Cuba's gambling operations, and exerted influence over Batista's casino policies. The Mafia's Havana Conference was held on December 22, 1946, at the Hotel Nacional de Cuba; this was the first full-scale meeting of American underworld Leaders since the Chicago meeting in 1932. Lansky set about cleaning up the games at the Montmartre Club, which soon became the "place to be" in Havana. He also wanted to open a casino in the Hotel Nacional, the most elegant hotel in Havana. Batista endorsed Lansky's idea over the objections of American expatriates such as Ernest Hemingway, and the renovated casino wing opened for Business in 1955 with a show by Eartha Kitt. The casino was an immediate success.

He continued to participate in Cuban politics, and was elected to the Cuban Senate in absentia in 1948. Returning to Cuba, he decided to run for President and received permission from President Grau, whereupon he formed the United Action Party. On taking power he founded the Progressive Action Party, but he never regained his former popular support, though the unions supported him until the end.

In a manner that antagonized the Cuban people, the U.S. government used its influence to advance the interests of and increase the profits of the private American companies, which "dominated the island's economy". By the late 1950s, U.S. financial interests owned 90% of Cuban mines, 80% of its public utilities, 50% of its railways, 40% of its sugar production and 25% of its bank deposits—some $1 billion in total. According to Historian Louis Perez, author of the book On Becoming Cuban, "Daily life had developed into a relentless degradation, with the complicity of political Leaders and public officials who operated at the behest of American interests." As a symbol of this relationship, ITT Corporation, an American-owned multinational telephone company, presented Batista with a Golden Telephone, as an "expression of gratitude" for the "excessive telephone rate increase" that Batista granted at the urging of the U.S. government.

On March 10, 1952, three months before the elections, Batista, with army backing, staged a coup and seized power. He ousted outgoing President Carlos Prío Socarrás, canceled the elections and took control of the government as a provisional President. The United States recognized his government on March 27. When asked by the U.S. government to analyze Batista's Cuba, Arthur M. Schlesinger, Jr. said

On July 26, 1953, just over a year after Batista's second coup, a small group of Revolutionaries attacked the Moncada Barracks in Santiago. Government forces easily defeated the assault and jailed its Leaders, while many others fled the country. The primary leader of the attack, Fidel Castro, was a young attorney who had run for parliament in the canceled 1952 elections. Although Castro was never officially nominated, he felt that Batista's coup had sidetracked what would have been a promising political career for him. In the wake of the Moncada assault, Batista suspended constitutional guarantees and increasingly relied on police tactics in an attempt to "frighten the population through open displays of brutality."

Batista held an election in 1954, running as the candidate of a political coalition that included the Progressive Action Party, the Radical Union Party and the Liberal Party. The opposition divided into abstentionists and electoralists. The abstentionists favored boycotting the elections regardless of the circumstances in which they were held, whereas the electoralists sought certain rights and guarantees to participate. The CIA had predicted that Batista would use any means necessary to ensure he won the election. Batista lived up to their expectations, utilizing fraud and intimidation to secure his presidency. This led most of the other parties to boycott the elections. Former President Ramón Grau San Martín, leading the electoralist factions of the Cuban Revolutionary Party, participated through the political campaign but withdrew from the campaign days before election day, charging that his supporters had been terrorized. Thus Batista was elected President with the support of 45.6% of registered voters. Despite the boycott, Grau received the support of 6.8% of those who voted. The remaining voters abstained.

Batista encouraged large-scale gambling in Havana. In 1955, he announced that Cuba would grant a Gaming license to anyone who invested US$1 million in a hotel or $200,000 in a new nightclub—and that the government would provide matching public funds for construction, a 10-year tax exemption, and waive duties on imported equipment and furnishings for new hotels. Each casino would pay the government $250,000 for the license, plus a percentage of the profits. The policy omitted background checks, as required for casino operations in the United States, which opened the door for casino Investors with illegally obtained funds. Cuban contractors with the right connections made windfalls by importing, duty-free, more materials than needed for new hotels and selling the surplus to others. It was rumored that, besides the $250,000 to obtain a license, an additional "under the table" fee was sometimes required.

In April 1956, Batista called popular military leader Col. Ramón Barquín back to Cuba from his post as military attaché to the United States. Believing Barquín would support his rule, Batista promoted him to General. However, Barquín's Conspiración de los Puros (Conspiracy of the Pure) was already underway and had already progressed too far. On April 6, 1956, Barquín led hundreds of career officers in a coup attempt, but was frustrated by Lieutenant Ríos Morejón, who betrayed the plan. Barquín was sentenced to solitary confinement for eight years on the Isle of Pines, while some officers were sentenced to death for treason. Many others were allowed to remain in the military without reprimand.

Batista's resignation as President on New Year's Eve 1958–59 is reenacted in a pivotal scene in the Academy Award–winning 1974 film The Godfather Part II, although the Cuban President is not named. The role was played by Tito Alba. Batista was also depicted in the 1979 film Cuba and in the 2005 film The Lost City.

As news of the fall of Batista's government spread through Havana, The New York Times described jubilant crowds pouring into the streets and automobile horns honking. The black and red flag of July 26 Movement waved on cars and buildings. The atmosphere was chaotic. On January 8, 1959, Castro and his army rolled victoriously into Havana. Already denied entry to the United States, Batista sought asylum in Mexico, which also refused him. Portugal's dictator António Salazar allowed him to settle there on the condition that he completely abstain from politics.

According to Historian and author James S. Olson, the U.S. government essentially became a "co-conspirator" in the arrangement because of Batista's strong opposition to communism, which, in the rhetoric of the Cold War, seemed to maintain Business stability and a pro-U.S. posture on the island. Thus, in the view of Olson, "The U.S. government had no difficulty in dealing with him, even if he was a hopeless despot." On October 6, 1960 Senator John F. Kennedy, in the midst of his campaign for the U.S. Presidency, decried Batista's relationship with the U.S. government and criticized the Eisenhower administration for supporting him:

After he fled to Portugal, Batista lived in Madeira, then later in Estoril, outside Lisbon. He was the Chairman of a Spanish life insurance company that invested in property and mortgages on the Andalusian Costa del Sol. He died of a heart attack on August 6, 1973, at Guadalmina, near Marbella, Spain, two days before, allegedly, a team of assassins from Castro's Cuba were to carry out a plan to assassinate him.

Marta Fernández Miranda de Batista, Batista's widow, died on October 2, 2006. Roberto Batista, her son, says that she died at her West Palm Beach, Florida home. She had suffered from Alzheimer's disease. She was buried with her husband and son in Cementerio Sacramental de San Isidro in Madrid, after a Mass in West Palm Beach.

As the new hotels, nightclubs, and casinos opened, Batista collected his share of the profits. Nightly, the "bagman" for his wife collected 10% of the profits at Santo Trafficante's casinos, the Sans Souci cabaret, and the casinos in the hotels Sevilla-Biltmore, Commodoro, Deauville, and Capri (partly owned by the actor George Raft). His take from the Lansky casinos—his prized Habana Riviera, the Hotel Nacional, the Montmartre Club, and others—was said to be 30%. Lansky was said to have personally contributed millions of dollars per year to Batista's Swiss bank accounts.