The 28-year-old model and the Puerto Rican rapper, 29, were last seen together at the 'Saturday Night Live' afterparty in October after the music star hosted and performed in an episode of the late-night sketch show.
An insider told People that the pair have gone their separate ways.
A source also told ETOnline: "Kendall and Bad Bunny have been doing their own things lately and things slowly started to fizzle out between them."
They continued: "They both knew going into this that it likely wouldn't be a forever type of relationship and that was mutually understood from the get-go.
"They have crazy busy schedules and know they're still young and have a lot more to experience individually before settling down."
It was an amicable split with the insider adding that there "isn't any negativity between them and they still want the best for one another."
The couple tried to keep their relationship as private as possible, with Bunny refusing to confirm their romance.
Speaking on the rumours previously, he told Rolling Stone magazine: "I know something is going to come out. I know [people are] going to say something. People know everything about me, so what's left for me to protect? My private life, my personal life."
Asked if there is anything he wants to clarify about his relationship status and romance with Kendall, the 'Where She Goes' hitmaker insisted he wants to keep some parts of his life private.
He added: "That's the only answer. In the end, the only thing I have is my privacy."
Meanwhile, Kendall recently revealed she is keen to have children.
Speaking about her family plans, she said on 'The Kardashians': "Three max - I'm cool with two, though. I just want my kid to, for sure, to have a sibling. I know that."
Kris Jenner, 68, Kendall's mom, would also love her daughter to start a family.
However, the model insists she's not in any rush.
Kendall said: "I swear I got this, and I will give you a grandkid when the time is right, and when it all makes sense perfectly."