HSA vs. FSA: What’s the Difference and How Does It Affect Your Taxes? If you have medical expenses, both an HSA and an FSA can help you save money but they work very differently when it comes to taxes and rules. HSA (Health Savings Account) Think of an HSA as a medical savings account that belongs to you. • You must have a high-deductible health plan to qualify • Money you put in is tax deductible • The account rolls over every year you don’t lose it • You can keep it even if you change jobs • W