Just to be clear, an employee with an employer-sponsored HSA can make either kind of employee HSA contribution: through payroll deduction with the employer, and also after-tax contributions directly from the employee that can then be taken as an above-the-line tax deduction. The direct employee contributions would suffer the same FAFSA treatment as similar HSA contributions from self-employed workers. Hence my remark above that for those who want to contribute to an employer-sponsored HSA and are expecting to use federal student aid, they should, as much as possible, make their employee contributions through pre-tax payroll deductions.