Chepngetich, who smashed the record in Chicago last October, was provisionally suspended in July this year by the Athletics Integrity Unit after Hydrochlorothiazide (HCTZ) was detected in a sample collected from the Kenyan athlete on March 14.
The sample revealed an HCTZ concentration of 3,800ng/mL, far above the World Anti-Doping Agency's minimum reporting limit of 20ng/mL.
Chepngetich initially denied any wrongdoing and could not explain the positive result despite an AIU investigation, which included analysis of her medications, supplements and phone data.
Chepngetich changes explanation for positive test
However, on July 31, two weeks after Chepngetich was suspended, she changed her explanation, saying she had unknowingly taken her housemaid's medication, which contained HCTZ, while ill.
The AIU said HCTZ is used clinically to treat fluid retention and hypertension, adding that diuretics may be abused to mask the presence in urine of other prohibited substances.
The AIU said Chepngetich's actions were reckless and indirectly intentional rather than accidental, initially applying a four-year sanction.
However, Chepngetich's early admission earned her a one-year reduction, resulting in a three-year ban issued on September 10.
"The case regarding the positive test for HCTZ has been resolved but the AIU will continue to investigate the suspicious material recovered from Chepngetich's phone to determine if any other violations have occurred," AIU head Brett Clothier said in a statement.
"In the meantime, all Chepngetich's achievements and records pre-dating the 14 March 2025 sample stand."
Reuters has contacted Chepngetich's representative for comment.
High-profile doping cases
In April, Chepngetich had withdrawn from the London Marathon, saying she was "not in the right place mentally or physically" to run her best, but she had actually opted for a voluntary provisional suspension at the time.
Marathon running has been hit with a spate of high-profile doping cases in recent years, particularly from Kenya which is world renowned for its middle and long-distance runners.
In November 2022, the middle and long-distance running powerhouse avoided a ban despite an increasing number of its athletes being suspended for positive tests.
Athletics Kenya had said its government pledged $5 million per year for five years to fight doping in athletics.
In February 2024, Kenya's Sarah Chepchirchir was hit with an eight-year ban after the former Tokyo Marathon winner was found to have violated anti-doping regulations for a second time when she returned an adverse analytical finding for testosterone.
Earlier this year, Kenyan marathon runner Brimin Kipkorir - who won the Sydney Marathon in 2024 in a course record time -- was also provisionally suspended by the AIU after he tested positive for prohibited substances.