London's Metropolitan Police force said Katsutoshi Jitsukawa appeared at Uxbridge Magistrates' Court in west London and admitted exceeding the alcohol limit.
Tests found the 42-year-old first officer had 189 milligrams of alcohol per 100 millilitres of blood in his system, nearly 10 times the 20 milligrams limit for a pilot.
The driver of a crew bus at Heathrow Airport noticed the smell of alcohol on the co-pilot's breath and reported it to police, according to JAL.
Tests found the 42-year-old first officer recorded 0.18 blood-alcohol reading, nearly 10 times the legal limit for a pilot and four times the amount for driving.
The drink-drive limit in England, Wales and Northern Ireland is 80mg, compared to 20mg for pilots. From Haneda, it takes about 12 hours and 30 minutes to fly to London, but 11 hours and 45 minutes for the return flight.
He had reportedly consumed two bottles of wine and more than 1.8 litres (nearly four USA pints) of beer over six hours on the night before the flight.
His aircraft - a Boeing 777, which holds up to 244 passengers - was delayed by more than an hour after his arrest.
JAL have apologised for the incident and said: "Steps will be taken to prevent future occurrences".
The incident came just a day after All Nippon Airways revealed a hung-over pilot had caused multiple flight delays.
"We are certain (the in-house breath test) wasn't conducted properly", Muneaki Kitahara, JAL's head of communications, told a press conference.
Toshinori Shin (C), general manager of Japan Airlines Co.'s Flight Operations Division, bows in apology at a press conference in Tokyo on November 1, 2018.
The male pilot in his 40s called in sick after a night of drinking on the remote resort island of Ishigaki in southern Okinawa prefecture, the company said.