The $28 is a separate fee, but it's not a one time according to their faq
Can I buy a membership for more than one year? Are there discounts?
Clear is available for $100 plus a $28 TSA vetting fee, for a total of $128 per year. Lock in these prices by purchasing a two-year membership for $256 or a three-year membership for $384. Your Clear card will work at any US airport with a registered traveler program at no additional cost.