Originally named Boriquén by the Taino Indians, Puerto Rico was settled by several Indian groups long before it was visited (1493) by Christopher Columbus on his second voyage to the New World and renamed San Juan Bautista. It was given its present name, meaning "Rich Port," by Juan Ponce de León, who established a settlement inland from San Juan at Caparra in 1508. Although the dominant Taino then numbered about 30,000, the Indian population, decimated by forced labor and losses from rebellion, had virtually disappeared by 1582.

The Spaniards introduced sugarcane to the island in 1511, and the first black slaves arrived in 1518. In the centuries that followed, the colony grew slowly, as the Spanish concentrated on the richer colonies of Mexico and Peru. During the late 16th century the island's strategic value was realized, and Spain began to fortify it, holding it against frequent English, French, and Dutch attacks into the 19th century. Not until the late 18th century, when Spain lifted trade restrictions, did Puerto Rican commerce begin to develop. By that time the black slave population was significant. According to the population census carried out by the Spaniards in 1765, there were 5,037 black slaves (12.7% of the total population). By 1846 the number had increased to 51,265, or 13.08% of the total population. In 1860, when the last census was taken before the slaves were freed in 1873, the number of slaves had declined to 41,738, or 7.7% of the total population.

Spain, which had granted Puerto Rico almost complete autonomy by 1897, ceded the colony to the United States in 1898 after the Spanish-American War; it was under U.S. military rule from 1898 to 1900. The first U.S. population census of the island, taken in 1899, found that Puerto Rico had nearly a million people. The governor and legislature were federally appointed until 1917, when the Jones Act made all Puerto Ricans U.S. citizens and created an elected senate. Puerto Rico did not elect its own governor until 1948. The commonwealth was established in 1952.

In 1948, Luis Muñoz Marín, Puerto Rico's first popularly elected governor, initiated "Operation Bootstrap" to improve the economy. Tax incentives and low labor costs attracted large- and small-scale industries, providing the underpinnings for an economic transformation over later decades. Per-capita income rose dramatically, although unemployment remained high and wages low compared to the U.S. mainland. The cornerstone of the plan was federal tax exemptions. Establishments operating with these tax breaks became known as the 936 firms, relating to the exemptions in section 936 of the U.S. tax code.

An economic slump in the early 1980s increased demands for greater autonomy. Subsequently the economy picked up, but Hurricane Hugo in 1989 brought renewed economic hardship to Puerto Rico, as did a cutback in federal tax breaks in 1993. In August 1996 the U.S. Congress voted to eliminate tax-exemption privileges for firms in Puerto Rico, a move that brought much uncertainty as to the future of the 936 firms. Another recent source of worry for government officials has been possible adverse effects of the globalization trends and the North American free trade agreements.

The New Progressive party won the governorship and legislative majorities in the election of 1992, and in January 1993, a law was enacted making both Spanish and English official languages. Later in 1993 the long-standing issue regarding Puerto Rico's political status was again considered when a plebiscite was held in which Puerto Rican voters could choose statehood, the commonwealth status in place since 1952, or independence. By a narrow margin the voters opted to maintain the commonwealth. The New Progressive party retained power in the elections of 1996 with a gubernatorial victory and legislative majorities in both houses. In the summer of 1998 the governor and island legislature authorized another referendum on statehood for December. In the nonbinding status referendum, the majority voted for options other than statehood, with the procommonwealth Popular Democratic party urging followers to vote for "none of the above," the option that took 50.2% of the vote. Other voter options were statehood (46.5%), independence (2.5%), and commonwealth and free association (less than 1% each).

In September 1998, Puerto Rico was struck by the powerful Hurricane Georges, which swept over the island bringing death, property damage, flooding, power outages, and a lack of potable water. The damage sustained from the storm has been estimated at about $2 billion.

In a controversial decision in September 1999, President Bill Clinton, in an act of clemency, freed 11 members of a Puerto Rican nationalist group who had been jailed in federal prisons around the country. Those released belonged to a Puerto Rican independence organization responsible for 130 bombings in the late 1970s and early 1980s. They were released after vowing to renounce terrorism. None had been convicted of crimes involving deaths or injuries.

Beginning in the spring of 1999 a U.S. Navy bombing range on Puerto Rico's Vieques Island was the scene of a year-long occupation by protestors who have called for an end to naval bombing on the island. The occupation occurred following the death of a civilian guard, killed when two 227-kg (500-lb) bombs were accidently dropped. After months of negotiations, President Clinton in January 2000 issued a directive allowing for the resumption of military exercises with inert ammunition and calling for a referendum that would either let the navy resume use of the range on its own terms or require the navy to cease all training by May 2003. The referendum was to be held on May 1, 2001, or 270 days earlier or later. In May 2000 federal agents expelled more than 200 protesters from the range, and in June the navy again began shelling exercises. Protests continued in early 2001, and in June the George W. Bush administration announced a halt to all military exercises and aerial bombing on Vieques by May 2003. A referendum had been scheduled for July 29th.

In November 2000 elections there was a return to power of the Popular Democratic party, which won the gubernatorial office, legislative majorities, and the lone seat in the U.S. Congress. The San Juan mayoral office, however, was won by a member of the New Progressive party.