Manipal University offers various scholarships and loan facilities. Scholarships are available for top-ranked students: those within the top 10 ranks receive scholarships, and students within the top 500 ranks are eligible for merit-based scholarships. Free-ship is available for students within the top 100 ranks. Konkani-speaking students receive an annual scholarship of INR 10,000, and there are specific scholarships for Academy General Education students (SAGES). Scholarships based on NEET ranks are available, with full scholarships for ranks up to AIR 2000 and partial scholarships for ranks up to AIR 5000.
The university also collaborates with banks like SBI and ICICI to provide student loans at low interest rates, up to INR 15 lakhs without security. Tuition fees are structured based on parental income and rank, with annual fees for a general seat around INR 17.8 lakhs and additional fees for hostel accommodations. NRI students have separate fee structures. Scholarships and loans are available to facilitate education, encouraging academic excellence.

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