The boxing champion and Faryal are said to be dividing their time between Dubai and the United Kingdom.
The separation is the latest scandal in the couple’s ten-year marriage.
“Faryal is taking time to think about whether or not to walk away,” a source close to the Khan family said.
“She’s going through a very difficult time and is choosing to focus on her children while she and Amir continue to co-parent.”
It comes after It was revealed that Amir begged wedding beauty Sumaira to send him intimate photos. After first contacting her in May to admire her tattoos, the boxer attempted to meet up with her.
In one message, he said, “look good on g string” and indicated she had a boob job.
Weeks later, Khan, who married Faryal in 2013, posted a photo of himself with his US model wife and daughters on Instagram, captioning it “10 years later.”
He later admitted that he was willing to go to counselling to stop sexting other women. Khan also apologised to his wife, who had questioned him, “If you have a diamond at home, why do you want to mess around with rocks and stones?”
In the aftermath of the scandal, the I’m a Celebrity contestant also whisked Faryal away on a romantic trip to Mykonos.
In another scandal, a former BBC presenter has accused the retired boxer of making sexual advances towards her after they appeared at an event together.
Suzi Mann, who has presented BBC Asian Network's Official Asian Music Chart Show, claims she was sent messages by Khan, 36, after they first met in 2016 when she hosted a concert in Manchester.
She said that following their encounter, Khan repeatedly messaged her on WhatsApp 'flirting' with her and 'making sexual advances', which later escalated when he began calling and leaving her voicemails.
The single mother said in a post to her over 19,000 followers on Instagram that she did not feel 'comfortable' with his messages and she "remained professional" by choosing not to "entertain" his behaviour.
Earlier this week, a new woman also claimed she had an affair with the boxer over four months - which only ended when Faryal threatened to 'name and shame' her.
The unnamed woman has revealed that the champion fighter admitted his marriage was 'on the rocks' and said that she slept with him this year after he demanded 'no holds barred' sex.
The woman reportedly said she met with Amir on several occasions, but that their fling ended when she received a call from his furious wife.
The couple have gone through a tumultuous time recently after Faryal posted a lengthy statement in response to her husband's text exchanges with model Sumaira.
Stating that she 'refuses to play out my marriage publicly,' Faryal wrote on Instagram that 'after a long week of accusations, slander and harassment I have decided it is now time to address the situation that has unfolded.'
Faryal described Sumaira's actions as a 'hate campaign' and has denied that she is 'responsible for Sumaria's current mental state.'
Implying that she is standing by Amir, Faryal went on to state that 'the whole world is aware of his track record' and insists that Sumaira must have been aware he was married when she sent him revealing photos.