The origins of the current flag of Puerto Rico, adopted by the Commonwealth of Puerto Rico in 1952, can be traced to 1868, when the first Puerto Rican flag, "The Revolutionary Flag of Lares", was conceived by Dr. Ramón Emeterio Betances and embroidered by Mariana "Brazos de Oro" Bracetti. This flag was used in the short lived Puerto Rican revolt against Spanish rule in the island, known as "El Grito de Lares".

Juan de Mata Terreforte, an exiled veteran of "El Grito de Lares" and Vice-President of Puerto Rican Revolutionary Committee, in New York City, adopted the Flag of Lares as the flag of Puerto Rico until 1892, when the current design, modeled after the Cuban flag, was unveiled and adopted by the committee. The new flag, which consisted of five equal horizontal bands of red (top and bottom) alternating with white; a blue isosceles triangle based on the hoist side bears a large, white, five-pointed star in the center, was first flown in Puerto Rico on March 24, 1897, during the "Intentona de Yauco" revolt. The use and display of the Puerto Rican flag was outlawed and the only flags permitted to be flown in Puerto Rico were the Spanish flag (1492 to 1898) and the flag of the United States (1898 to 1952).

In 1952, the Commonwealth of Puerto Rico adopted the same flag design, which was unveiled in 1892 by the Puerto Rican Revolutionary Committee, as its official standard without specifying the tones of colors to be used. The color of the triangle that was used by the administration of Luis Muñoz Marín was the dark blue that is used in the flag of the United States, instead of the original light blue, thus creating a political controversy which has lasted throughout the years. In 1995, the government of Puerto Rico, issued a regulation in regard to the use of the Puerto Rican flag titled: "Reglamento sobre el Uso en Puerto Rico de la Bandera del Estado Libre Asociado de Puerto Rico" in which the government specifies the colors to be used but, does not specify any official color tones or shades. Therefore, it is not uncommon to see the Flag of Puerto Rico with different shades of blue displayed in the island. Several Puerto Rican flags were aboard the Space Shuttle Discovery during its flight into outer space on March 15, 2009.

Each of the 78 municipalities of Puerto Rico have adopted flags which represent the region and its people. Most of the designs of these flags derive their symbolism from the regions Coat of Arms. Most of the political parties in Puerto Rico also have their own flags, which represent and symbolize the political ideals of its members. These flags are usually displayed in public during rallies, meetings, or parades in show of political strength and unity. Various sports associations in Puerto Rico have adopted flags which represent them and which are also used during competitions and sports events.

The introduction of a flag in Puerto Rico can be traced to when Christopher Columbus landed on the island's shore and with the flag appointed to him by the Spanish Crown claimed the island, which he named "San Juan Bautista", in the name of Spain. Columbus wrote in his logbook that on October 12, 1492 he used the Royal Flag, and that his captains used two flags which the Admiral carried in all the ships as Ensign, each white with a green cross in the middle and an 'F' and 'Y', both green and crowned with golden, open royal crowns, for Ferdinand II of Aragon and Ysabel (Isabel I). The conquistadores under the command of Juan Ponce de León proceeded to conquer and settle the island. They carried as their military standard the "Spanish Expedition Flag". After the island was conquered and colonized, the flag of Spain was used in Puerto Rico, same as it was used in all of its other colonies.

Once the Spanish armed forces established themselves on the island they began the construction of military fortifications such as La Fortaleza, Fort San Felipe del Morro, Fort San Cristóbal and San Gerónimo. The Spanish Army designed the "Burgundy Cross Flag" and adopted it as their standard. This flag flew wherever there was a Spanish military installation.

The independence movement in Puerto Rico gained momentum with the liberation successes of Simón Bolívar and José de San Martín in South America. In 1868, local independence leader Ramón Emeterio Betances urged Mariana Bracetti to knit a revolutionary flag using the flag of the Dominican Republic as an example. The flag was divided in the middle by a white Latin cross, the two lower corners were red and the two upper corners were blue with a white star in the upper left blue corner. According to Puerto Rican poet Luis Llorens Torres the white cross on it stands for the yearning for homeland redemption; the red squares, the blood poured by the heroes of the rebellion and the white star in the blue solitude square, stands for liberty and freedom. The "Revolutionary Flag of Lares" was used in the short-lived rebellion against Spain in what became known as El Grito de Lares (The Cry of Lares). The flag was proclaimed the national flag of the "Republic of Puerto Rico" by Francisco Ramírez Medina, who was sworn in as Puerto Rico's first president, and placed on the high alter of the Catholic Church of Lares, thus becoming the first Puerto Rican Flag. The original Lares flag was taken by a Spanish army officer as a war prize. Many years later it was returned and transferred to the Puerto Rican people. It is now exhibited in the University of Puerto Rico's Museum.

In 1873, following the abdication of Amadeus, Duke of Aosta, as King (1870–1873) and with Spain's change from Kingdom to Republic, the Spanish government issued a new colonial flag for Puerto Rico. The new flag, which was used until 1873, resembled the flag of Spain, with the difference that it had the coat of arms of Puerto Rico in the middle. Spain's flag once more flew over Puerto Rico with the restoration of the Spanish kingdom in 1873, until 1898 the year that the island became a possession of the United States under the terms of the Treaty of Paris (1898) in the aftermath of the Spanish-American War.

Juan de Mata Terreforte, a leader of the Grito de Lares revolt who fought alongside Manuel Rojas, was exiled to New York City. He joined the Puerto Rican Revolutionary Committee and was named its Vice-President. Terreforte and the members of the Revolutionary committee adopted the Flag of Lares as their standard. In 1892, the Committee was presented with the design of the current flag of Puerto Rico. The new flag's design has been attributed to various Puerto Ricans who were members of the Puerto Rican Revolutionary Committee in New York City.

Some sources document Francisco Gonzalo Marín with presenting a Puerto Rican flag prototype in 1895 for adoption by the Puerto Rican Revolutionary Committee in New York City. Marín has since been credited by some with the flag's design. There is a letter written by Juan de Mata Terreforte which gives credit to Marin. The original contents of the letter in Spanish are the following: