Both these premiere Indian institutes are academically at par with each other. But you should consider these points when choosing between the two-

1. JIPMER is located in Pondicherry and has no airport connecting it to metropolitan Indian cities. For the nearest airport, you’ll have to travel all the way to Chennai.
2. Pondicherry is much safer though. You can walk alone in the evenings without any fear.
3. JIPMER is much bigger than MAMC. Also, JIPMER provides top notch hostel facilities, at par with private colleges. Its campus is very well maintained as well.
4. The JIPMER campus is so huge that students use scooties and bikes to travel from one block to another.
5. MAMC offers more variety for North Indian meals. 
6. At MAMC, patients speak Hindi. At JIPMER on the other hand, Tamil is the dominant language. So there is some communication gap initially, but one learns to manage with time.
7. Delhi offers a better city life, more malls and better movie theaters. Pondicherry is a calm and serene place with beautiful beaches. There aren’t huge shopping malls and big multiplex theaters over there, but you’ll be mesmerized by its natural beauty. 

Both the colleges are equally excellent. You must choose between them based on your personal preference.

First and foremost you should know that both MAMC (Maulana Azad Medical College) and JIPMER (Jawaharlal Institute of Postgraduate Medical Education and Research) are amazing institutes. It is bit tough to decide which college is better but still I would help you in understanding the facts on which you can decide which college to choose:

• To get into one of the colleges you have to be a good scorer in NEET which is crucial.
• Geographically, the students who want to go for North India and he/she who has a good score, approach Maulana Azad Medical College at first. As the environment is quite conducive.
• Contrast to this, those students who belong from Southern Part of India prefer JIPMER as they get the same atmosphere as their home.

But let me assure you that getting into either of the institutes is a pride for a student. And there is no other factor to say no to any of the colleges. So you can take admission in either and move forward.