The 49-year-old Chicago man was charged this week for helping plot the terror attack in Mumbai a year ago that killed 166 people.
Federal authorities, already suspicious of him, used his return to the U.S. this summer as an opportunity, according to officials.
A border inspector asked Mr. Headley about his overseas travel, according to court records and people familiar with the case.
Mr. Headley said he was working for a company called First World Immigration Service. First World is a business that allegedly provided Mr. Headley with cover as he traveled to scout terrorist targets for Lashkar-e-Taiba, the group responsible for the November 2008 assault in Mumbai, according to the federal charges.
Agents searched Mr. Headley's luggage and found it "contained no papers or other documents relating to such a business," according to court documents. They also searched tax records and found no record of income paid to Mr. Headley by the company, court records show.
Mr. Headley was returning to the U.S. from a trip to Denmark in which he was scouting potential targets, authorities alleged. He is also being charged with planning an armed assault on a Danish newspaper that published cartoons of the Muslim Prophet Muhammad.
Authorities said little more about the airport interview, including where it happened or why they had become suspicious of Mr. Headley. But court records showed that federal surveillance of Mr. Headley, who is an American, accelerated afterward.
Mr. Headley's case is the most potent example of a U.S. born radical. Law enforcement and terrorism specialists said Lashkar's alleged deployment of Mr. Headley underscored the usefulness of recruits with U.S. passports in terror plots.
Mr. Headley traveled to India and Pakistan over nearly two years to videotape targets and brief his co-conspirators in the Mumbai attacks, according to the federal charges.
Westerners have largely played supporting roles in terror activities, but Mr. Headley's ability to travel freely on a U.S. passport to Pakistan, India and Denmark gave him high value, a U.S. law enforcement official said.
"It's exactly the way you'd think al Qaeda would want to use operatives," said Evan Kohlmann, who has testified on Lashkar as an expert witness in U.S. and British courts.