The school's study system provides a wide range of opportunities for students to pursue their own interests and to prepare them for the academic challenges of higher education. The school has three major departments: humanities, life sciences, and maths and physics. Every department offers a set of subjects with the aim to provide a well-rounded education in the specific area of study.

In addition to attending regular academic classes, students must also attend practical classes related to their chosen area of study. The subjects are taught in Estonian. There are also elective courses and extracurricular activities, such as choir and folk dancing.

At Hugo Treffner Gymnasium it is possible to choose between three departments:                                                          

Department of Humanities

The humanities students focus on literature, history and culture.

• Literature - an extended learning programme and practical classes
• History - an extended learning programme
• History of Art
• Philosophy
• Informatics
• Modern Languages (English, Russian, German, French, Swedish)
• Civics

• Religious studies                                                                                                                                                                                                                                                   

​Department of Life Sciences

Having chosen this direction, students will receive a deeper knowledge of biology and chemistry.

• Biology - an extended programme and practical lab classes
• Chemistry - an extended programme and practical lab classes
• Food Technology
• Maths - an extended programme
• Philosophy
• Modern languages (English, Russian, German)

• Latin                                                                                                                                                                                                                                                   

Department of Maths and Physics

The maths and physics department sets the main focus on mathematics, physics and informatics.

• Physics – an extended programme and practical classes
• Informatics - basic courses for programming
• Maths – an extended programme and practical classes
• Various technology courses;

• Modern languages (English, Russian, German) _