In a court filing, the FTC asked a federal judge in Georgia to stop FleetCor and Chief Executive Officer Ronald Clarke, from charging hidden fees and to disgorge ill-gotten gains.
In its complaint, the FTC said that FleetCor had marketed payment cards to companies with fleets of vehicles, promising that they would save money, that there would be fraud controls, and that there were no membership or transaction fees.
But it said that after customers had signed up, FleetCor charged them "at least hundreds of millions of dollars in unexpected fees."
FleetCor said in a statement that it disagreed with the FTC, adding the "complaint is based upon fundamental misconceptions of the company, its customers and its products."
The company said its customer disclosures are "clear and communicated repeatedly, and that its customers are "sophisticated businesses who read their contracts, invoices and reports."
J.P. Morgan estimated in an analyst note that the disputed fees were likely less than 3% of revenue.
When customers noticed the charges and complained to FleetCor, the company removed the charges, and "in many instances FleetCor has begun charging these customers for different fees to make up the difference," the FTC said in its complaint.
The FTC also accused the company of billing customers for interest, finance charges and programs to which they had not consented.
The FTC said that tens of thousands of customers had complained to government agencies and/or the Better Business Bureau.
The company's share price closed up 0.5 percent.
(Reporting by Diane Bartz, Editing by Rosalba O'Brien and Grant McCool)