The 21-year-old model stars in the drinks company's 'Jump In' promotional film, which has been accused of co-opting the Black Lives Matter campaign by some social media users.
In the short film, Kendall skips out of a photoshoot to join a protest alongside placard-waving campaigners, before she offers a can of Pepsi to one of the surly-looking police officers as a sign of peace.
The commercial has been accused of trivialising a serious issue by some of its online critics, but Pepsi has defended the advert, saying it carries an "important message".
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In a statement to E! News, the company said: "This is a global ad that reflects people from different walks of life coming together in a spirit of harmony, and we think that's an important message to convey."
Kendall joined Pepsi Max's Live For Now moments campaign earlier this week, with the American model saying the brand reflected her eagerness to embrace every moment in life.
She said: "I am thrilled to join the legendary roster of icons who have represented their generations and worked with Pepsi.
"To me, Pepsi is more than just a beverage it registers as a pop culture icon and a lifestyle that shares a voice with the generation of today."
Kendall claimed she was excited to appear in the campaign because it chimed with her own outlook.
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The 'Keeping Up with the Kardashians' star explained: "The spirit of Pepsi living in the 'now' moment- is one that I believe in. I make a conscious effort in my everyday life and travels to enjoy every experience of today."
The short film also features music from Jamaican singer-songwriter Skip Marley, who released his debut single 'Lions' in February 2017.
Skip whose single appears on the moments advert said: "Standing together and being unified in the moment is a powerful experience.
"This song 'Lions' that Pepsi selected for the 'Moments' ad should remind our generation to look at the way you are living and find strength and calm in each moment."