The pair were spotted in a car outside fast food restaurant Wendy's upon being reunited in Cody, where the rapper has been staying at his $14 million ranch.
And in pictures obtained by DailyMail.com, Kim looked visibly upset during a conversation with the 43-year-old star.
A source told PEOPLE: ''She decided to fly to Cody to speak to him in person. She doesn't want to be ignored anymore.''
The pair's reunion comes after he claimed on social media last week that he has been trying to divorce Kim after she allegedly met Meek Mill at a hotel.
He also likened Kim's mother, Kris Jenner, to North Korean leader Kim Jong-un, and explained he had ''almost killed'' his daughter North, now seven, because the pair had considered getting an abortion.
Kanye - who also has kids Saint, four, Chicago, two, and Psalm, 14 months, with the 'Keeping Up with the Kardashians' star - said sorry to his wife over the weekend, admitting he regretted ''going public with something that was a private matter''.
Taking to Twitter hours after he was visited on his ranch by Justin Bieber, he wrote: ''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. (sic)''
Kanye did not explain which comments he was specifically apologising for.
Last week, Kim, 39, described Kanye as a ''brilliant but complicated person'', and spoke about his bipolar disorder publicly for the first time.
She wrote: ''As many of you know, Kanye has bi-polar disorder. Anyone who has this or has a loved one in their life who does, knows how incredibly complicated and painful it is to understand. I've never spoken publicly about how this has affected us at home because I am very protective of our children and Kanye's right to privacy when it comes to his health.
''But today, I feel like I should comment on it because of the stigma and misconceptions about mental health. Those that understand mental illness or even compulsive behavior know that the family is powerless unless the member is a minor. People who are unaware or far removed from this experience can be judgmental and not understand that the individual themselves have to engage in the process of getting help no matter how hard family and friends try.
''I understand Kanye is subject to criticism because he is a public figure and his actions at times can cause strong opinions and emotions. He is a brilliant but complicated person who, on top of the pressures of being an artist and a Black man, who experienced the painful loss of his mother and has to deal with the pressure and isolation that is heightened by his bi-polar disorder.
''Those who are close with Kanye know his heart and understand his words sometimes do not align with his intentions. Living with bi-polar disorder does not diminish or invalidate his dreams and his creative ideas, no matter how big or unobtainable they may feel to some. That is part of his genius and as we have all witnessed, many of his big dreams have come true. We as a society talk about giving grace to the issue of mental health as a whole, however we should also give it to the individuals who are living with it in times when they need it the most. (sic)''
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