Margaret Ngotho (born 25 June 1970) is a Kenyan former long-distance runner who competed in cross-country running and track events.
Her highest achievement was a bronze medal in the short race at the IAAF World Cross Country Championships in 2000.
She was three times a team medalist at the competition for Kenya, winning gold in 1991 and 1995 then finally silver in 2001.
She was a double bronze medallist at the African Championships in Athletics in 1990, running the 3000 metres and the 1500 metres.
She was a three-time Kenyan champion, winning at both track distances and once in short cross country.