The 43-year-old rapper was reported to have been staying in the bunker of his Wyoming mansion leaving his children with Kim Kardashian at home in Los Angeles.
The couple’s oldest son, 4-year-old Saint, was pictured on the stairs of the plane as the family waited to take off.
It is likely that Kim and Kanye’s other children – 7-year-old North, 2-year-old Chicago, and 14-month-old Psalm – were already on board.
Kim, 39, and Kanye’s marriage has faced difficulty in recent weeks with the reality star said to be “torn” over divorcing Kanye.
Sources previously said that Kim has “tried everything” and her kids are the priority.
They added to People: “She isn’t getting back what she needs from Kanye.
“She was to the point that she flew to Cody to basically tell him their marriage is over and to say goodbye.”
Kim was seen crying in the car with Kanye on Monday after the rapper apologized for divulging personal details about their marriage.
The star claimed he’d been trying to divorce Kim for two years, and stopped his wife from aborting their daughter North.
Acknowledging he was wrong in sharing such personal matters with the world, he tweeted: “I would like to apologize to my wife Kim for going public with something that was a private matter.
“I did not cover her like she has covered me. To Kim I want to say I know I hurt you.
“Please forgive me. Thank you for always being there for me.”
But sources say Kanye has yet to take steps to repair their relationship, as he referenced considering aborting his oldest child again on social media this weekend.
He wrote: “I cried at the thought of aborting my first born and everyone was so concerned about me…
“I’m concerned for the world that feels you shouldn’t cry about this subject.”
The insider says: “He doesn’t seem to get what she is saying. He hasn’t changed anything that she told him needs to change.