Most AFLAC policies are accident and health insurance, not medical insurance.  They wouldn't qualify for deduction or exempt you from ACA provisions.

Checking to see how this could properly be setup in Quickbooks online, as a deduction. Quickbooks community "experts" are telling folks to setup as health insurance, medical. If this wont qualify as medical that would cause issues with false totals on the W2 at the end of year. I am not sure the best way to work around this, since they only provide choices of Medical, Dental or vision when you choose Health Insurance. 

Yes, you can set up your Aflac payments up as health insurance if it is a policy that exclusively pays medical costs. 

As bwa points out, some Aflac plans cover other types of events like accidents and disability, those are not health insurance plans. 

Aflac offers plans that pay amounts for specific medical events, like hospitalization, or a doctor visit. These plans are considered health insurance for both payroll and tax purposes. 

If you aren't sure if your policy is considered health insurance, check with your agent or contact the company directly.