Fogle was seen at his Zionsville, Indiana, home during the search this morning.
Authorities would not elaborate on the nature of the investigation, though it comes two months after the executive director of Fogle's foundation, Russell Taylor, was arrested on child pornography charges.
Fogle's attorney told ABC News in a statement that his client has not been charged with any crime.
"Jared has been cooperating, and continues to cooperate, with law enforcement in their investigation of unspecified charges, and looks forward to its conclusion," attorney Ron Elberger said in the statement.
Subway issued a statement about the investigation involving the longtime face of the company.
"We are shocked about the news and believe it is related to a prior investigation of a former Jared Foundation employee. We are very concerned and will be monitoring the situation closely," the company said in its statement.
Taylor faces eight preliminary federal felony charges, including multiple counts of possession of child pornography, voyeurism and child exploitation. Taylor remains in jail, according to federal documents. It was not immediately clear whether Taylor has entered a plea. Federal prosecutors have until August to impanel a grand jury, according to Taylor’s lawyer.
At the time of Taylor's arrest, Fogle released a statement to the Indianapolis Star condemning Taylor.
"I was shocked to learn of the disturbing allegations against Mr. Taylor. Effective immediately, the Jared Foundation is severing all ties with Mr. Taylor," Fogle said in the statement.
Fogle, 37, gained national fame when he lost a significant amount of weight by eating turkey and vegetable sandwiches from Subway and exercising. He was first featured in ads for the company in 2000 and he launched The Jared Foundation in 2004, with a mission to improve children's health.
ABC News' Aaron Katersky contributed to this report.