The 31-year-old is hot favourite to be crowned the best player in the world for the fourth time.
However, Ronaldo was on board when Madrid players took off to Tokyo Haneda at 7am UK time, from Adolfo Suarez Madrid-Barajas Airport on Saturday night.
All the players in the squad were on the flight, except for Gareth Bale, who is out for four months after ankle surgery.
They are expected to arrive 5.30am local time on Monday, which is 8.30pm UK time, following a 13-and-a-half hour flight.