HTG was founded in 1883 as a private school for boys by Hugo Hermann Fürchtegott Treffner.

1883 - On 7 December 1883, Hugo Treffner was granted permission to found his own school, which began operating in January 1884. It was a school with three junior secondary grades (pro-gymnasium) and German as the language of instruction.
1886 - A house on Hobuse Street became the location of the school.
1889 - Russian became the language of instruction.
1890 - The school was granted the rights of an 8-class gymnasium
1907 - Hugo Treffner received the name and rights for a private gymnasium.
1912 - Hugo Treffner died and the school was taken over by his widow and several teachers.
1917 - Konstantin Treffner, a distant relative of Hugo Treffner, was appointed headmaster.
1918 - From the autumn of 1918, classes were taught in Estonian.
1919 -  In February, the school moved to its present building on the corner of Rüütli and Munga Streets, the largest school in Estonia at the time. Part of the former Aleksander Gymnasium was merged with the school.
1933 - The 50th anniversary of the school was celebrated. The celebrations were also attended by  head of state Konstantin Päts.
1940 - The school was renamed Secondary School No. 4. 
1944 - The school was merged with Tartu I Gymnasium to form Tartu Secondary School No. 1, which operated in the same building.
1954 - The former boys' secondary school became a co-educational school.
1958 - The school was named Anton Hansen Tammsaare Tartu Secondary School No. 1. 
1961 - The first specialized mathematics class in Estonia was opened.
1964 - A specialized physics class was opened. 
1965 - The first Five Schools Competition was held, although initially only with the then A.H. Tammsaare Tartu Secondary School No. 1, C. R. Jakobson Viljandi Secondary School No.1 and Nõo Secondary School. Miina Härma Tartu Secondary School No. 2 and Tartu Secondary School  No. 5 joined the competition in 1967.
1969 - The specialized math and physics classes were merged into one science class. 
1977 - The primary classes moved into the "small house" at Lai Street 28 (present-day Kesklinna School).
1984 - The 100th anniversary of the founding of Hugo Treffner Private Gymnasium was celebrated with a conference in the assembly hall of the University of Tartu and a concert by the students at Vanemuine Theatre.
1989 - With the support of alumni, Hugo Treffner's gravestone was restored in Uue-Jaani cemetery (sculpted by 1977 alumnus Mati Karmin). The first life sciences class was opened.
1990 - The historical name of the school was restored - Hugo Treffner Gymnasium.
1994 - A course system was introduced, admission to form 7 ended. 
1996 - A humanities class was opened. 
1997 - The Hugo Treffner statue (sculptor Mati Karmin) was opened to the public in Emajõgi Park, and from 1 September the school became a fully three-grade gymnasium.

1998 - On 16 November, the schoolhouse was damaged by a fire.

1999 - Renovations of the school building began. 
2000 - The school was moved back into the partly renovated building.
2001 - A new gym was opened.
2002 - The renovation of the school building was completed in September.

Headmasters of HTG:

Hugo Treffner 1883-1912
Vladimir Usbenski 1913-1914
Nikolai Sahharov 1914-1917
Konstantin Treffner 1917-1940
Johannes Valgma 1940-1941
August Raielo 1941-1944
Karl Maasik 1944-1950
Juhan Truus 1950-1953
Elmar Loodus 1953-1956
Allan Liim 1956-1970
Uno Langer 1970-1975
Laine Raudsepp 1975-1987
Helmer Jõgi 1987-2001
Ott Ojaveer 2001-

Compiled based on historical overviews by history teachers Eeva-Eili Kask, Maia Käpp, and extracurricular activities director Uve Saar.