The Computer Science and Engineering (CSE) study program, established in 2004, is the oldest and first computing-related program at the university. IUS also started three double diploma programs in Computer Engineering with Marmara University, Istanbul University, and Istanbul Technical University between 2023 and 2024, showing its commitment to international collaboration and quality education. The timeline below, titled "Key Milestones in the Development of the IT Programs at IUS," highlights the launch of CSE as a major milestone, alongside other program introductions, international partnerships, and important infrastructure advancements.

The CSE study program falls under the Technical Sciences area, specifically within the Information and Computing Engineering field. Most core courses align with the scientific branches of Computer System Organization, Software Engineering, and Computing Methodologies, forming the foundation of the bachelor and master programs. In addition to these core branches, the CSE study program also include compulsory courses from the branches of Theoretical Mathematics, Applied Mathematics, and Probability and Statistics within the field of Mathematics.

The CSE study program is designed in a way that it provides comprehensive and interdisciplinary education in the computer science and engineering field that shapes graduates who can address the contemporary challenges in the global and local business and scientific environment. Aside from the academic component, the program emphasizes collaboration with industry and training students to seamlessly integrate into the current business environment. The variety of topics studied under the CSE includes, but is not limited to, programming, mathematical foundations of computer science, databases, computer architecture, algorithms, user-interface design, web development, operating systems, computer networks, cybersecurity, data mining, etc.

The graduates of the CSE program are trained to be able to work both in industry and pursue further specialization in academia. By the end of their studies, students will possess the necessary training to fulfill all responsibilities that come with being project managers, programmers, scientists in industry, or professors at a university.