NCE has offered the BE Computer Engineering program since the college's establishment in 2001 A.D., meeting the growing demand for skilled computer engineers in Nepal and the global technology sector. The program is designed to produce highly skilled, innovative, and industry-ready computer engineers, combining computer science, electronics, software engineering, communication systems, artificial intelligence, networking, and embedded systems. It aims to develop technically competent, ethically responsible, and globally competitive graduates who can contribute to national development and technological advancement, following the updated 2080 syllabus.

Facilities for students in the Computer Engineering program:

• Dedicated laboratories for practical, drawing, and design work
• Workshops and bootcamps as part of the "Practice" stage of learning
• Field visits as prescribed in the syllabus to connect theory with real-world systems
• Project-based learning, including site visits and project presentations
• Structured learning pathway across four stages: Foundation, Core Computer, Practice, and Capstone
• Core coursework spanning Programming, Computation, Database Management, Software Engineering, and Artificial Intelligence
• Laboratory & practical courses making up 35% of the program (theory at 65%)
• Specialization tracks including AI & Machine Learning, Data Science & Analytics, Cybersecurity, Cloud Computing, Computer Networks, and Human Computer Interaction