Which engineering branch should I choose among CSE and IT?

Considering the syllabus, there is not much difference between two branches but yes CSE is more preferred by recruiters than IT

would suggest you to take CSE.As far as I have noted, CSE students get to learn core computer Science papers while IT more of general stuffs. They never had Detailed Algorithms or theory of computation which are of more importance in GATE or related exams.Some companies specifically wanted only CSE