In 1997 the school moved into one wing of the Tallinn Medical School, gaining a proper cafeteria, gym, playground and assembly hall. The first grade 9 class opened in the autumn of 1998. By that time the number of students had grown to 70.
ISE began its affiliation with the International Baccalaureate Organization (IBO) in 2003 when the school became an authorized IB Diploma school in the spring, with PYP authorization following in the fall.
1999 saw major changes in the organisation of the school with the registration of a new legal entity, the non-profit organisation International Educational Association of Estonia (MTU IEAE), which would operate three schools – International Preschool of Estonia, International School of Estonia and International Gymnasium of Estonia.
In 2000 the school moved into the centre of Tallinn, first sharing the building with another school and in the following year becoming the sole tenant of a two-story building owned by the Ministry of Education. The century-old building, a former military barrack and stable, had been renovated as a cooking school in the 1960s.
The new century saw the number of students rise above one hundred. Grade 10 was first formed in 2000, and these students would continue on each year until 2003 when they became the first high school graduates of the International School of Estonia. ISE graduated its first IB Diploma class in the spring of 2005.
In 2004 at the Annual General Meeting of the Association, the decision was accepted that the International Gymnasium of Estonia was to be united with the International School of Estonia. From that point on, MTÜ IEAE has operated two schools – the International Preschool of Estonia (Preschool 3, 4 and Reception) and the International School of Estonia (Grades 1 – 12).
Beginning in 2005 ISE expanded its physical education program with an arrangement to use the facilities at Tallinna Spordihall . The summer of 2007 saw the school’s largest building project with the complete renovation of the school library. A two-year playground project was begun in the summer of 2009, and a interior renovation was begun in 2010.
As of the 2016-17 school year, ISE enrolls approximately 150 students, offering a comprehensive education to children ages 3 to 19 years (Pre-school to Grade 12) who wish to maintain continuity with their home country education or to join with an English-speaking program.
The school is operated on a non-profit basis by a Board of Directors elected annually by the parents of children in the school. Parents participate in the life of school by serving on school committees, organizing extra-curricular activities and volunteering in the school. The ISE Parent Teacher Association is actively involved in organizing school events.