The first course devoted to electronic computers at University of Tartu - "Problems of Contemporary Computer Technology" - was delivered by Ülo Kaasik in the spring term of 1957. Subsequently, the first computer centre in Estonia was established under the initiative of the Head of the Chair of Geometry at the University of Tartu in 1959. The first computer was Ural-1. In the same year the new speciality - applied mathematics - was opened.
The Institute of Computer Science was established during the reorganization of the Chair of Programming in 1993 which had been established in 1979. The first Head of the Institute in 1993 was Docent Jaanus Pöial. From 1 January 2003 to 31 December 2010 the Head of the Institute was Docent Tiit Roosmaa. Since 1 January 2011 the Head of the Institute is Prof. Jaak Vilo.
The Institute is located in a renovated building at J. Liivi Street 2, Tartu.