Maathai and her husband, Mwangi Mathai, separated in 1977. After a lengthy separation, Mwangi filed for divorce in 1979. Mwangi was said to have believed Wangari was "too strong-minded for a woman" and that he was "unable to control her". In addition to naming her as "cruel" in court filings, he publicly accused her of adultery with another Member of Parliament,^[29] which in turn was thought to cause his high blood pressure and the judge ruled in Mwangi's favor. Shortly after the trial, in an interview with Viva magazine, Maathai referred to the judge as either incompetent or corrupt.^[29] The interview later led the judge to charge Maathai with contempt of court. She was found guilty and sentenced to six months in jail. After three days in Lang'ata Women's Prison in Nairobi, her lawyer formulated a statement which the court found sufficient for her release. Shortly after the divorce, her former husband sent a letter via his lawyer demanding that Maathai drop his surname but she instead chose to add an extra "a" instead.^[30][31]

The divorce had been costly, and with lawyers' fees and the loss of her husband's income, Maathai found it difficult to provide for herself and her children on her university wages alone. An opportunity arose to work for the Economic Commission for Africa through the United Nations Development Programme. As this job required extended travel throughout Africa and was based primarily in Lusaka, Zambia, she was unable to bring her children with her. Maathai chose to send them to her ex-husband and take the job. While she visited them regularly, they lived with their father until 1985.