Yes, I believe you can pursue a PhD after MCA. Ideally if you aim to pursue a PhD in Computer Science/IT/Software related subjects, it will be beneficial to have a Valid GATE CSE as well as UGC NET (JRF) Score with you. Besides this you need to apply/mail to the respective professor for Research Positions at relevant time, before start of session. There is a definite admission procedure for both falls in different Institutes for Junior Research Fellowship.