Before they left, the country’s President Muhammadu Buhari and Vice-President Yemi Osinbajo met the squad of 25 and senior officials in the capital Abuja.
The players will be joined in England by Chelsea midfielder Victor Moses, who was given an extended break after a hectic season with the Premier League side.
Injury doubt Moses Simon, from Belgian side Gent, was on the flight and will have a third scan to determine the extent of a hamstring injury he suffered recently in training.
Super Eagles coach Gernot Rohr has dropped four players from his provisional 30-man squad: goalkeeper Dele Ajiboye, defenders Stephen Eze and Uche Agbo, and forward Junior Lokosa.
Rohr will whittle down the squad to 23 after the match at Wembley on Saturday.
Nigeria are due to attend a final training camp in Austria and a final friendly against the Czech Republic on June 6, before heading to Russia on June 11.
The three-time African champions have been drawn in Group D with Argentina, Croatia and Iceland. Their first game is on June 16 against Croatia in Kaliningrad.