Salary is paid by the company to an employee who is on their payroll whereas stipend is to help with a specific expense.
Criteria for payment of salary should meet the Minimum Wages Act whereas Payment of stipend is based on the National Apprenticeship Promotion Scheme (NAPS) and the education level.
Salary Payments include benefits such as health insurance and deductions like statutory deductions whereas a stipend is normally a fixed sum without any deductions or benefits.