On 1 April 1940, Maathai was born in the village of Ihithe, Nyeri District, in the central highlands of the colony of Kenya, then part of the British Empire. Her family were Kikuyu, the most populous ethnic group in Kenya, and had lived in the area for several generations. Around 1943, Maathai's family relocated to a white-owned farm in the Rift Valley, near the town of Nakuru, where her father had found work. Late in 1947, she returned to Ihithe with her mother, as two of her brothers were attending primary school in the village, and there was no schooling available on the farm where her father worked. Her father remained at the farm. Shortly afterward, at the age of eight, she joined her brothers at Ihithe Primary School.
At the age of eleven, Maathai moved to St. Cecilia's Intermediate Primary School, a boarding school at the Mathari Catholic Mission in Nyeri. Maathai studied at St. Cecilia's for four years. During this time, she became fluent in English and converted to Catholicism, taking the Christian name Mary Josephine. She also was involved with the Christian society known as the Legion of Mary, whose members attempted "to serve God by serving fellow human beings." Studying at St. Cecilia's, Maathai was sheltered from the ongoing Mau Mau Uprising, which forced her mother to move from their homestead to an emergency village in Ihithe. When she completed her studies there in 1956 she was rated first in her class, and was granted admission to the only Catholic high school for girls in Kenya, Loreto High School Limuru in Limuru.After graduating from Loreto-Limuru in 1959, she planned to attend the University of East Africa in Kampala, Uganda. However, the end of the colonial period of East Africa was nearing, and Kenyan politicians, such as Tom Mboya, were proposing ways to make education in Western nations available to promising students. John F. Kennedy, then a United States Senator, agreed to fund such a program through the Joseph P. Kennedy Jr. Foundation, initiating what became known as the Kennedy Airlift or Airlift Africa. Maathai became one of about three hundred Kenyans chosen to study at American universities in September 1960