The accident occurred at around 3 a.m. on Monday near a junction of the Metropolitan Expressway in Yokohama City.
The victim was identified as Patrick Do, a resident of California, who took part in the Cycle Messenger World Championships held from Wednesday through Monday in the city, the event's organizers said.
The organizers said the event had ended by the time of the accident and they speculate the 31-year-old was returning to his hotel.
The driver of the car told police that the cyclist appeared in front of him so suddenly that he was unable to stop in time.
Navigation apps blamed for leading bicycles, scooters onto expressways
Bicycles and small motorcycles are not allowed on expressways in Japan.
But the Metropolitan Expressway Company confirmed 419 cases last fiscal year in which pedestrians, cyclists, and motor scooter riders mistakenly entered the Metropolitan Expressway.
Among the cases of cyclists and scooter riders, about 60 percent of them were mistakenly directed onto the expressway through navigation apps.
Company officials are urging people to set navigation apps to the appropriate mode and to frequently check the actual road signs.
Foreigners account for more than 10 percent of mistaken entries on expressways
There have also been cases of foreigners who mistakenly entered an expressway. The Metropolitan Expressway Company says around 13 percent of total cases involved people who did not speak Japanese.
To prevent such mistakes, expressway operators have placed large signs in English, or in simple Japanese, at entrances and exits on highways.
Some entrances have cameras that detect a wrong entry by pedestrians, cyclists or scooter riders and issue a warning through voice or electric bulletin boards.
Highway operators are calling on people who see a wrong entry on an expressway to call the road emergency number at #9910.