Ms Cheptegei was reportedly rescued by neighbours after the incident at her home in the small village of Endebes on Sunday.
She was targeted while returning from church with her two children.
Local police chief Jeremiah Ole Kosiom told reporters the attacker suffered severe burns.
The two are being treated at the Moi Referral Hospital in Eldoret, the region's main city.
“A couple was heard arguing outside the house. During the argument, the boyfriend was seen pouring liquid on the woman and setting her on fire,” Mr Kosioum was quoted as saying.
Mr Cheptegei, who hails from an area just across the Ugandan border, is said to have bought land and built a home in Trans Njoia County, near many of Kenya's sports training centres.
According to a report filed by local officials, the two were fighting over land. Police said an investigation is underway.
Mr. Cheptegei recently finished 44th in the marathon at the Paris Olympics.
She also won a gold medal at the 2022 World Mountain and Trail Running Championships in Chiang Mai, Thailand.
In April 2022, another female runner, Damaris Mutua, was found strangled with a pillow over her face in a house in Iten village in the Rift Valley.
The incident comes just months after long-distance runner Agnes Tirop, who set a new world record, was found stabbed to death in the same village.
In both incidents, authorities identified their partners as the main suspects.
Ms Tirop's husband is now accused of murder, which he denies, and the search for Ms Mutua's boyfriend continues.
Men have also been targeted.
In December last year, another Ugandan athlete, Benjamin Kiplagat, was stabbed to death by assailants in Eldoret.
