Fees at JSS Medical College and Hospital for the Bachelor of Medicine, Bachelor of Surgery (MBBS) program differ based on the admission category. For management quota seats, the tuition fee is approximately 18.5 to 19.86 lakh rupees per annum with additional first-year fees of 1,36,400 rupees, totaling 19,86,000 rupees. For subsequent years, the tuition remains at 18,50,000 rupees with other fees of 38,400 rupees per annum. Government quota seats require a tuition fee of around 1 lakh to 1,44,496 rupees per annum.
NRI quota fees range from 33 lakh to 40 lakh rupees annually. Hostel accommodation incurs an additional annual fee of approximately 1,50,000 rupees. Scholarships are available based on NEET UG results, primarily benefiting Karnataka quota students, while other reserved category students do not receive fee reductions. The tuition fees during the internship year amount to half the usual annual rate, approximately 9,25,000 rupees.

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The fee for the Master of Science (M.Sc) in Medical Biochemistry is INR 2,24,000 for the duration of 2 years which includes various charges such as registration fees, tuition fees, etc. The entrance schedule for the course is not out yet.