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The origins of the school can be traced back to a private school, Numune-i Terakki Mektebi, founded in 1884 by Mehmet Nadir Bey, a retired Navy Captain. The Nummune-i Terakki Mektebi, which opened in a mansion adjacent to the Mashihat Office near Süleymaniye, was a seven-year school providing education at the level of ibtidai, rüşdiye and idadi for boys in the years of its establishment, and later on, the girls' class was also included. Numune-i Terakki, the first student magazine in the Ottoman Empire, was published for nine issues during this period with the contributions of Mehmet Nadir Bey. This private school, which continued its educational activities first in Çırçır and then in a mansion in Fatih, was closed by the palace in 1896 and its administration was placed under state control.

Under the administration of the Ministry of Education, the school was moved to mansions in Laleli, Saraçhanebaşı and Kantarcılar, and its duration was reduced to five years in 1908 when the iptidai and rüşdiye grades were combined. In 1909, the school was moved to the Darülfünun and Mekteb-i Mülkiye building and its name was changed to "İstanbul Leyli İdadisi".

The name of the school was changed again in 1910 and became "Istanbul High School for Boys" ("İstanbul Erkek Lisesi"). Thus, this school became the first educational institution in Turkey to use the word "High School" ("Lise). In 1911, Nijat, one of the students of the school, created the first emblem of his school by combining the letters "elif" and "sin" with a crescent star. The scout organization called Keşşaf, an important innovation in the history of education in Istanbul, was founded by physical education teacher Ahmet Robenson in 1912.

Realizing that the school had become one of the most popular educational institutions in Istanbul, the Committee of Union and Progress (İttihat ve Terakki) administration decided to protect the Istanbul Boys' High School, just as the administrators of the Tanzimat period had protected the Galatasaray Sultanisi and ensured the spread of French culture in the past. In 1913, the French curriculum was introduced at the school and its name was changed to "Istanbul Sultanisi". During this period, Alaeddin and his assistant Fuat Beys organized a movie theater at the school, a first in the history of education. The first movie was Les Miserables, the story of Jac. The educational activities of Saint Benoit High School, a French school, were terminated before World War I. In 1914, the Istanbul Sultanate moved to the Saint Benoit building in Karaköy.

During the war, part of the school was converted into a hospital and painted yellow as a sign of hospitalization. Many students of the school had gone to the front and fought in both the Balkan and World War I. Students who went to the front and were wounded were treated at the school hospital. When the news came that fifty students had been martyred at Kanlısırt on the Çanakkale Front, the doors of the school were painted black. Yellow and black became the school's colors from that day on.

In 1917 it was decided that the language of instruction would be German. Twenty-two teachers were brought from Germany. However, after World War I, when the German Empire was forced to withdraw its support for schools abroad, German education at the Istanbul Sultanate was suspended.

After the signing of the Armistice of Mondros, the school was evacuated by the occupation forces; it was transferred to the girls' school in Haşimpaşa Mansion, then to Mercan Idadisi, and in 1919 to Münirpaşa Mansion in Saraçhanebaşı. In 1922, the scouting organization was re-established. The scouts who voluntarily participated in the Battle of Sakarya returned as veterans. When Mustafa Kemal Pasha addressed them as "Children of Sakarya", the scouts changed their name to "Sakarya Scout Troop" and the Sakarya Anthem became the school anthem.

The Sultani period of the school ended in 1923. The school was renamed "Istanbul High School for Boys" and moved to the Fuat Pasha Mansion in Beyazıt. In 1933, the school moved to its current building, formerly used as the Düyûn-ı Umûmiye (state debts) building, with the directive of President Mustafa Kemal.

With the initiatives of Hüseyin Celal Yardımcı, one of the 1926 graduates of the school, German-language education resumed at Istanbul High School for Boys in 1955. In 1964, female students were again admitted to the school.

In 1982, the school became an Anatolian High School and its name was changed to "Istanbul High School". In 1998, due to the 8-year uninterrupted education reform, the school stopped admitting students to the middle school and became a 5-year educational institution with one year of preparation. In 2019, the name of the school was changed back to its more common and well-known name "Istanbul Erkek Lisesi" as a result of the efforts of Fatih Güldal, the former school principal who took office in 2018.