The two posed for a snap at Thursday's ESPY Awards, (Excellence in Sports Performance Yearly) which were held at the Microsoft theatre in LA in California.
While Amir, 31, posted another clip of them on Instagram, correctly labelling her as Caitlyn, 68, fans did not hold back when it came to criticising the boxer.
Gaffe: Amir Khan has been accused of transphobia after labelling Caitlyn Jenner 'Bruce' on social media despite her changing her name legally three years ago
They wrote: 'Amir Khan is not funny for calling Caitlin Jenner Bruce he demonstrates what a transphobic c*** he is. And I don't even like Caitlin Jenner.' [sic].
'Amir Khan calling Caitlyn Jenner 'Bruce Jenner' at the #ESPYS though !!! KILLED ME!'
'Still dying at the fact that amir khan called Kaitlyn Jenner BRUCE.' [sic]
MailOnline has contacted a spokesperson for both Caitlyn Jenner and Amir Khan for comment.
Caitlyn underwent gender reassignment surgery in January 2017, almost two years after she revealed her decision to transition.
Something to say: Fans were not impressed that Amir had called Caitlyn Bruce and labelled him transphobic as a result
Jenner publicly revealed she had transitioned in a 20/20 interview back in April of 2015 with Diane Sawyer, telling the veteran newscaster: 'For all intents and purposes, I am a woman.'
She went on to say in that interview: 'My brain is much more female than it is male. That's what my soul is. Bruce lives a lie. She is not a lie. I can't do it anymore.'
That June, Jenner appeared on the cover of 'Vanity Fair' wearing a white satin bustier with the words: 'I Am Caitlyn.'
Sporting great: Caitlyn (pictured as Bruce in 1976) giving a victory salute after the 1500m discipline of the Decathlon event at the Olympic games in Montreal, Canada
Got it right this time: Amir also shared this picture on Instagram and correctly tagged 'Caitlyn Jenner'
Caitlyn, who as Bruce, won the 1976 Olympics decathlon event at the Montreal Olympic Games, changed her name officially on September 25, 2015.
Amir's blunder follows a series of gaffes made by the professional boxer.
Last year, when appearing on I'm A Celebrity, Amir was accused of 'casual sexism' when he asked if the UK has ever had a female Prime Minister.
Despite Theresa May being in power, the boxing star left fans reeling when he asked the 'idiotic' question.
Viewers also accused him of 'casual sexism' after he called Georgia Toffolo a 'small little girl' while assessing her Kung Fu technique.
Right then: Amir Khan sparked outrage on I'm A Celebrity last year, after asking if a woman can be Prime Minister – despite Theresa May currently being in power
Oh dear: The boxing star left fans reeling when he had asked the question after learning that Georgia Toffolo had been appointed the jungle's deputy Prime Minister
Keep up! Theresa May has been the UK Prime Minister since June 2016
Need a history lesson? Margaret Thatcher led the country for more than ten years from 1979 until 1990
Amir sent Twitter into uproar after asking the camp: 'Has a woman ever become Prime Minister?'
As his campmates looked at him in disbelief and erupted with laughter, he hastily backtracked: 'Oh, Margaret Thatcher. S**t!'
Rebekah Vardy then told him that Theresa May is currently prime minister – to which he replied sheepishly: 'Oh and Theresa May. Guys don't tell no-one that.'
Theresa May has been the UK prime minister since June 2016 while Margaret Thatcher led the country for more than ten years from 1979 until 1990.
Is it laughable: Last August, Amir was forced to apologise to boxer Anthony Joshua, (pictured) for accusing him of cheating with his wife after he was threatened with legal action
Last August, Amir was forced to apologise to boxer Anthony Joshua for accusing him of cheating with his wife after he was threatened with legal action.
The heavyweight boxer got his advisers involved after a series of sensational tweets in which Khan shared supposed messages between Joshua and his wife online.
Faryal Makhdoom broke her silence on the public spat to reveal the Snapchat messages were fake, adding that she had never met Joshua.
After several social media digs between the pair, however, Amir and Faryal finally apologised over their very public falling out.
Shamed: Faryal Makhdoom broke her silence on the public spat to reveal the Snapchat messages were fake, adding that she had never met Joshua