The AIU said the sample, taken before her Sydney Marathon victory, tested positive for erythropoietin, a substance that boosts the production of red blood cells.
Her agent, Gianni Demadonna, said in an emailed statement: "I can only say that I feel terrible about what happened and I think it's only right that an athlete who uses the performance enhancing drugs should be disqualified."
Jepchirchir, 33, is one of the most decorated women in the sport, having won Olympic gold at the Tokyo Games in 2021 and claimed major marathon victories in New York (2021), Boston (2022), London (2024) and Sydney (2026). She previously held the half marathon world record.
She dominated the women's race in Sydney in August, finishing in 2:18:31, more than three minutes ahead of second-placed compatriot Irine Cheptai. The Sydney Marathon, which was added to the list of world majors beginning in 2025, said it was "extremely disappointed" by the news.
"Our commitment to clean sport is unwavering. Every athlete who lines up in Sydney deserves to race on a level playing field," the event said in a statement.
Jepchirchir is the latest in a long string of Kenyan athletes to fall foul of doping rules. More than 140 Kenyan athletes have been sanctioned since the AIU was established in 2017.
Olympic 10,000 metres silver medallist and broadcaster Kara Goucher, a whistleblower in the Nike Oregon Project case, said: "So much of what I see when I'm on a broadcast call I do not believe. I'm not surprised by this. I am, however, sad for all the athletes who finished behind her and were screwed out of a podium."
Last year, Kenya's women's marathon world record holder Ruth Chepngetich was banned for three years after admitting anti-doping rule violations involving the prohibited diuretic hydrochlorothiazide (HCTZ), though her world record of 2:09:56 remained on the books because it was set before her positive test.