Computer Science Institute (CSI) of Charles University was founded on January 1, 2012 as a part of School of Computer Science. Its main activity is research in theroretical computer science. It also actively contributes to scientific life by creating a continuing institutional background and administrative support, focusing on large research projects and other university-wide and international activities.

CSI builds upon more than twenty years of tradition and activity of the national research center ITI (later known as Center of Excellence ITI). It organizes Mathematical colloquia and publishes IUUK-CE-ITI preprint series, oversees the organization of regular conferences (STTI, MCW), organizes student exchanges (ERASMUS, REU), and has a leading role in the international center DIMATIA. CSI also coordinates the university center UNCE Center for Foundations of Modern Computer Science, and its activities also include ERC Synergy grant DYNASNET and other grant projects.

CSI actively supports research of doctoral students and significantly contributes to the organization of doctoral studies under the plan 4I4 Discrete models and algorithms. CSI members teach a number of basic and advanced courses at doctoral, masters', and bachelor's levels in the area of theoretical computer science and discrete mathematics, mainly in theory of algorithms, graph theory, calculus, optimization, and data structures.