Founded by Hugo Treffner, it was the only large secondary school in 19th-century Estonia with predominantly Estonian students and no age restrictions.

At the end of the year, a prep class was opened to teach languages and Treffner became a 4-class progymnasium.

[3]: 12  The school was named Vladimir Uspenski Private Gymnasium after Hugo Treffner died.

In the Estonian War of Independence, 230 students of Hugo Treffner Gymnasium were drafted, seven were killed in battle.

In 1933, the school celebrated its 50th birthday, which was attended by notable Estonian public figures, such as Jaan Tõnisson, Jüri Jaakson, Konstantin Päts, and others.

During the German occupation of 1941–1944, this school was closed and on 2 January 1942, Hugo Treffner Gymnasium was reopened, under the leadership of August Raielo.

Underground resistance groups such as "Blue-Black-White" (Sini-Must-Valge), named after the colours of the banned Estonian flag, were formed amongst the student body.

Popular were sport, music (including a jazz-orchestra), acting, art and natural sciences.

The position of school director was held by Allan Liim from 1956 to 1970, by Uno Langer from 1970 to 1975, by Laine Raudsepp from 1975 to 1987.

In 1976, the elementary school moved into a new building, the so-called "little house" ("väike maja").

With the Soviet Union nearing collapse in 1990, the school was once again officially named Hugo Treffner Gymnasium.

Since 1998, the school has been a gymnasium consisting only of forms 10 to 12, with the primary goal of preparing students for university.

[5]: 22  This solved the previous political arguments over restoring the historic schoolhouse, and a project to fully renovate the building was initiated.

In 2002, the project, which amounted to 82.32 million Estonian Crowns (5.26 mil euros), was successfully finished.

During the third week of April 2013 four German students and one teacher visited Estonia within the Comenius project.

[7][8] In October 2012, a student exchange program took place between the Lycée Léonard de Vinci and Hugo Treffner Gymnasium.

In March 2013, the Estonian students spent a week in France, where they were shown a piece of French people's local lives.

There they are shown the cities of Stockholm and Uppsala and they also take part in a friendly competition, where the teams consist of a mix of students from Estonia and Sweden.

The friendship with the Isokyrö School is mainly based on the choir and folk dancing groups of Hugo Treffner Gymnasium.

As the leaders of the choir and folk dancing groups were looking for a new destination, the Latvian school contacted Hugo Treffner Gymnasium with the wish to initiate a friendship.

Much like the trip to Isokyrö , the representatives of Hugo Treffner Gymnasium were mainly teachers, singers and dancers.

The Latvian students have been to Tartu only once, but they plan to come and visit Hugo Treffner Gymnasium once again in 2014.