From 1987 to 2001, the school director was Helmar Jõgi. With the Soviet Union nearing collapse in 1990, the school was once again officially named Hugo Treffner Gymnasium. The newly restored establishment was organised into a 6-class primary school and a gymnasium with a progymnasium. In 1995, the primary school and the progymnasium were merged into a separate school and Hugo Treffner Gymnasium stopped accepting students to the 7th form. Since 1998, the school has been a gymnasium consisting only of forms 10 to 12, with the primary goal of preparing students for university.