In the Americas, it is the first officially established (privilege by Charles V, Holy Roman Emperor) and the oldest continuously operating university.

Its official foundation was conceived by Fray Thomas de San Martín on May 12, 1551; with the decree of Emperor Charles I of Spain and V of the Holy Roman Empire.

In 2019, the "Colonial Fund and Foundational Documents of the National University of San Marcos: 1551–1852” was incorporated into the UNESCO Memory of the World Register.

[21][22] The National University of San Marcos is currently the leading Peruvian institution in scientific production, both annually[23] and cumulatively throughout history.

Due to its historical and academic significance, the National University of San Marcos is often referred to as the most important and representative educational institution in Peru.

The university moved to its second location, near the outskirts of San Marcelo, where the Convent of the Order of Saint Augustine had previously operated.

[13][50] The officially named University of San Marcos began its work in the viceregal era with the faculties of Theology and Arts,[51] later the canons of Law and Medicine would be created.

During the War of the Pacific and specifically during the occupation of Lima by Chilean troops, art and cultural objects and assets were taken from the university in order to be taken to Chile by sea.

A ceremony was also held that brought together the rectors of the main Ibero-American universities, who decided to give her the title of "Dean of America".

[64][65] As a tribute, on March 30, 2011, the university distinguished Vargas Llosa with its highest decoration: the San Marcos Medal of Honor in the degree of Grand Cross.

[68][69] Since its foundation until 1574, the first official shield showed an image of the Virgen del Rosario, considered the patron saint of the Dominican friars; on the right, a representation of the Pacific Ocean; and below a lime—fruit, referring to the city of Lima.

By the end of 1570, after the papal bull of Pius V, the coat of arms was modified, replacing the image of the Virgen del Rosario with that of the new patron of the university, the apostle Saint Mark and the Lion.

Although the use of a white flag with the shield of the university in the center had already been generalized, its use was recently made official through a rectoral resolution on June 14, 2010.

Among them are the Royal Certificate by which King Charles I of Spain authorized the foundation of the university in 1551, and the Quipu found in the Huaca San Marcos.

[72] The University of San Marcos was originally governed by clerics of monastic orders; during the Age of Enlightenment, the Bourbon Reforms transformed it into a secular institution.

[79] The University of San Marcos has 20 faculties grouped into 5 academic areas, in which 65 undergraduate programs, 77 master's degrees, and 27 doctorates are offered.

After the creation of the Royal College of Medicine and Surgery of San Fernando in 1811, it was installed as faculty on October 6, 1856, by Cayetano Heredia.

[80] In the National Medical Exams in Peru, the "San Fernando" Faculty of Medicine has obtained first place on numerous occasions.

In 1946, then President José Luis Bustamante y Rivero promulgated Law 10555, which created the Faculty of Chemistry at the University of San Marcos.

As there are a limited number of vacancies, an admission exam is carried out that is prepared and graded by a special jury according to the area of study to which it is applied.

[102] The University of San Marcos is actively involved in fostering international cooperation and engagement through various academic programs, research collaborations, and global partnerships.

At the end of the 19th century, the "San Fernando" Faculty of Medicine moved to its permanent location on the current Avenida Grau.

At the local level, it has been the official stadium of the university soccer team, Club Deportivo Universidad San Marcos, which played until 2011 in the Second Division of Peru.

[129] Below is a list of the main research institutes of the University of San Marcos:[127] Engineering: Humanities, and legal and social sciences: According to the 2009 annual balance prepared by the National Council of Science, Technology and Technological Innovation (CONCYTEC) of Peru, 20% of Peruvian scientific production was generated by the National University of San Marcos.

The complex is part of the area and the list of buildings in the historic center of the capital that in 1988 was declared a World Heritage Site by UNESCO.

At the end of the 18th century, the War Inspector Gabriel de Avilés y del Fierro dedicated the premises to the headquarters of the Royal Regiment of Lima.

Since the end of the 20th century, the University of San Marcos has given the Royal College the functions of a Cultural Center and Historical Archive.

[145][146] The word has been in common use by the Peruvian population to refer to the close and prominent figures of this house of studies, and even to the pets and animals adopted by the university community.

[156][157] The Stadium of the National University of San Marcos was the sole venue of the 2019 South American U-17 Championship that took place in Peru.

[158] José Rubio Galindo, a student at the Faculty of Letters, and Luis Málaga Arenas, a student at the Faculty of Medicine, would join Plácido Galindo, Eduardo Astengo, Rafael Quirós, Mario de las Casas, Alberto Denegri, Luis de Souza Ferreira (who scored the first Peruvian goal in a FIFA World Cup),[159] Andrés Rotta, Carlos Galindo, Francisco Sabroso, Jorge Góngora, Pablo Pacheco, Carlos Lassus and Carlos Cillóniz, among others.