The Department of Mathematics and Applied Mathematics of the University of Crete was established in June 2013 by the merger of the Department of Mathematics (founded in 1977) and the Department of Applied Mathematics (founded in 1999). The department accepts two incoming streams of undergraduate students (Mathematics, Applied Mathematics). It is simultaneously the oldest and the youngest department of the University of Crete and the largest department in the School of Science and Technology.

The program of mathematics offers a solid grounding on Mathematics during the first two years, with compulsory courses on Analysis, Linear Algebra, Algebra, Differential Equations, Probability, Computer Programming and Physics. After that the students may choose from a wide selection of courses in Pure and Applied Mathematics, as well as, courses from other departments (Physics, Computer Science, Biology, Economics, etc.) which will prepare them for postgraduate studies in Mathematics or other scientific domains. At the same time they may follow courses which will prepare them for a career in education.

The program on Applied Mathematics focuses on Analysis, Differential Equations, Probability, Statistics, Optimazation, Stochastic Processes, Numerical Analysis and Computational methods. It exposes students to the mathematical and computational techniques used in natural and engineering sciencesm through basic mathematics courses but also interdisciplinary courses, eg., Programming and Design of Algorithms, and through the study of mathematical models in fluid mechanics, material science, wave propagation and mathematical biology.