In 1989 a special group for hearing impaired children was opened in pre-school Pääsupesa. In 1991 another group was formed. Additionally, the first class for hearing impaired students was opened (2nd form). In 1992 another class was formed (3rd and 4th form). In 1993 the first form was opened (1st, 4th and 5th form).
On 1 September 1994 Tallinn Deaf School was opened as an independent educational institution. It started teaching according to the bilingual teaching method. There were four classes in school and two groups in pre-school. In the first year there were 34 children at the age of 3-15.
In 1995-1997 the schoolhouse was under reconstruction. In 1996/97 the first students finished basic school. Tallinn Deaf School started its work as an upper secondary school in autumn 1997. At the same time the boarding house was opened. In 1997/98 the basketball court of the school was opened.
In December 1999 the first service in Estonian Sign Language took place at the Church of the Holy Spirit.
In 2001 the first students finished upper secondary school.
In 2002 the extension of the schoolhouse was built. In the same year the integration group was opened in pre-school. The first sign language dictionary was published in 2003. In the same year the school started admitting hearing students. In summer 2005 the school received its new name after the famous deaf-blind woman Helen Keller. In the same year the blind students and blind students with multiple disabilities entered the school (2 pre-school groups, 1 coping class and a counselling centre for blind children).