"It turned out I guess I don't use it enough," Mr Obama said. "They thought there was some fraud going on."
Fortunately, he said, First Lady Michelle Obama had a credit card on hand and paid for the meal.
Mr Obama told the story at the Consumer Financial Protection Bureau as he announced new protections for debit cards used to deliver federal benefits.
An estimated 100 million Americans have been affected by identity theft in the past year, including high-profile security breaches at retailers like Target and Home Depot.
"I was trying to explain to the waitress, you know, I really think that I've been paying my bills," Mr Obama said. "Even I'm affected by this."
The US president is paid $400,000 (£250,000) per year, as well as given a non-taxable $50,000 expense account.