MCA is a post graduation course in computer application three year duration course . But B.E Computer Science engineering course is a graduation course in computer science.

In master of computer application course you will get theoretical knowledge in both hardware and software. But the B.tech CSE course is related to the application of the concepts.
B.E (Computer Science) students have more career opportunities than MCA candidates. The pay scale is also higher for B.E students.

Colleges for B.E Computer Science engineering
Indian Institute of Technology Bombay (IIT Bombay)
Indian Institute of Technology Delhi (IIT Delhi)
Birla Institute of Technology and Science (BITS-Pilani)
Indian Institute of Technology (IIT Guwahati)
National Institute of Technology, Tiruchirappalli
Indian School of Mines (ISM)
National Institute of Technology, Surathkal
Birla Institute of Technology..
Jadavpur University (Faculty of Engineering & Technology)
International Institute of Information Technology, Hyderabad (IIIT-H)
Netaji Subhas Institute of Technology
Motilal Nehru National Institute of Technology
PSG College of Technology
PEC University of Technology
Bengal Engineering and Science University
Malaviya National Institute of Technology
Visvesvaraya National Institute of Technology
Thapar University
Indian Institute of Technology Kanpur (IIT Kanpur)
Indian Institute of Technology Kharagpur (IIT KGP)
Indian Institute of Technology Madras (IIT Madras)
Indian Institute of Technology Roorkee (IIT Roorkee)
National Institute of Technology, Rourkela
College of Engineering Pune
Manipal Institute of Technology, Karnataka
Jawaharlal Nehru Technological University Hyderabad
R.V.College of Engineering
Veermata Jijabai Technological Institute
University College of Engineering (Osmania University)
Sri Sivasubramaniya Nadar College of Engineering - Tamil Nadu
Maulana Azad National Institute of Technology
Nirma University - Institute of Technology
BIT Sindri
Coimbatore Institute of Technology (CIT)
Vellore Institute of Technology (VIT)
Maharashtra Institute of Technology
National Institute of Engineering, Mysore
National Institute of Technology, Jamshedpur
BMS College of Engineering
National Institute of Technology, Durgapur
Amity School of Engineering and Technology
University Visvesvaraya College of Engineering - Karnataka
Amrita Institute of Technology and Sciences - Tamil Nadu
Chaitanya Bharathi Institute of Technology
College of Engineering Trivandrum
Bangalore Institute of Technology
SASTRA University
Jawaharlal Nehru Technological University, Kakinada
Thaigarajar College of Engineering
National Institute of Technology, Hamirpur
University Institute of Engineering & Technology
PES Institute of Technology
National Institute of Technology, Raipur
The Icfai Institute Of Science & Technology
National Institute of Technology, Patna
Gandhi Institute of Technology and Management (GITAM) University
Shri Ramdeobaba College of Engineering and Management
Sona College of Technology
Karunya University Request E-brochure
Dwarkadas J. Sanghvi College of Engineering

Colleges for MCA course
University of Pune
Jawaharlal Nehru University
University of Hyderabad
NIT
Birla Institute of Technology
NIT
Motilal Nehru National institute of Technology
PSG College of Technology
ITM University
Jamia Millia Islamia
University of Calcutta
Anna University of Technology
NIET School of Computer Science Applications
VIT University
BIT
NIT
Lovely Professional University
NMIMS University
Nirma University