The Secret Service are investigating the classified ad placed in Pennsylvania local paper the Warren Times Observer.
It said: "May Obama follow in the footsteps of Lincoln, Garfield, McKinley and Kennedy."
All four of the presidents named alongside Obama were assassinated.
Publisher John Elchert said it was removed as soon as a manager noticed the significance of the reference.
"It was just an honest mistake," he said.
An apology posted on the paper's website said the ad "apparently alludes to the wish that President Obama meet an untimely end".
The case has been handed to local police and the Secret Service, he added.
A spokesman for the Secret Service said they knew who placed the advert and were taking the threat seriously.
"We do not have the luxury of doing otherwise," Jim Mackin said.
President Obama has had 24-hour protection from the Secret Service since the early days of his campaign.