In 1872 a fund for Tallinna Peetri Reaalkool (Petri-Realschule zu Reval) was founded and in 1881 the school opened as a German-speaking school for boys. In 1884 the current school building was opened, being first purpose-built school in Tallinn and making it also one of the oldest schools in Tallinn. In the summer of 1881 the main subjects – Mathematics, Russian, Drawing, Geography, French, German and Science – were appointed by the School Board. In the first year, students were only accepted to the second and third grade. Next year, a fourth grade was opened where also English and Physics were taught. The first class graduated in 1885 with 6 students. One of them was Mihkel Vitsut, the first Estonian to have graduated from Tallinn Secondary School of Science.

In 1917, after the Russian February Revolution, PE teacher at Tallinn Secondary School of Science  Anton Õunapuu founded a Students Home Guard Squad. With their considerable aid, Estonian leaders and politicians were able to declare the independence of Estonia on the 24th February 1918.

The Estonian War of Independence against Soviet Russia began in Narva on 28th of November. At the outbreak of war every fourth soldier in Estonian defence forces was a student.

Approximately 100 soldiers in Estonian Independence War were from Tallinn Secondary School of Science. Four students and Anton Õunapuu gave their lives for the sovereignty of Estonia. Their names were carved in a marble plaque in 1923 which now is on display at the Tallinn Secondary School of Science’s assembly hall. In front of the school there is a sculpture in honour of all the student soldiers and teachers who lost their lives fighting for Estonia’s freedom. The sculpture is called Reaali Poiss („The Boy“ of the Science School).

In 1944 the II World War reached the Estonian soil. On March 9 and 10 Soviet army conducted their largest bombing raid in Tallinn’s history. As a result, almost ⅓ of the city was demolished. The schoolhouse was also among the buildings that got hit but weirdly enough „The Boy“ sculpture remained untouched. It stood in its place until 1948, when communists demolished it because the ideology it carried was not considered appropriate. On October 16,1944, the renamed and renovated, now called Tallinn Secondary School No. 2 opened its doors for students. An important change in the school took place in 1954 when the traditionally boys’ school was reorganised as a co-educational school and also girls were allowed to study at the school.

In 1989 the school’s name was changed back to Tallinn Secondary School of Science. In the spring of the same year the marble plaque with the names of Estonia´s Independence War heroes was reinstalled in the assembly hall. The official opening of the new Reaali Poiss („The Boy“ of the Science School’) sculpture took place in 1993.