As executive director of the United Nations Population Fund (UNFPA), Babatunde Osotimehin, who has died suddenly aged 68, provided a strong voice on issues affecting young women, including child marriage and female genital mutilation (FGM). He began the first of two four-year terms in the post in 2011, following high-profile roles in public health in his native Nigeria.

Despite his gentle demeanour, Osotimehin was tough when it came to pushing for commitments to improve family planning and maternal mortality rates. Much of his first term was concerned with upholding a global agreement negotiated in Cairo in 1994, designed to ensure greater access to education and family planning and to reduce child and maternal mortality.

He was also a fierce opponent of child marriage and FGM – two traditional practices that became the focus of his second term and the ending of which he characterised as “our unfinished business”. When he voiced his concerns, he liked to refer to himself as an “honorary woman” and he was a strong supporter of the Global Media Campaign to End FGM. At the time of his death he had been due to attend the New York premiere of the Guardian feature documentary on the subject, Jaha’s Promise, at the headquarters of the UN.

During his time at UNFPA, Osotimehin pursued three goals: to have no preventable maternal deaths, no unmet demand for family planning and to eliminate gender-based violence against women and girls. In support of the last of these, he managed a nine-year partnership with Unicef to reduce FGM across 17 countries, the largest programme in the world dedicated to ending the harmful practice that affects more than 200 million girls.

In tackling this issue and others, Osotimehin endorsed the use of culturally sensitive programmes run by local providers. He believed that if communities could engage in the programmes designed for their benefit, the positive effects would last much longer.

The organisation is funded mainly by governments and challenges arose when their visions did not meet his. Earlier this year, the Trump administration withdrew US funding, alleging UNFPA support for or management of “a programme of coercive abortion or involuntary sterilisation” in China, though the assertion has since been discredited.

Aside from a brief period under President Barack Obama during which the US was the UNFPA’s second largest donor, three of the last five US administrations have withheld funding, a challenge for which Osotimehin said he was prepared.

Babatunde was born in Ijebu Igbo, Ogun State, Nigeria, the eldest of eight children of Alaba Osotimehin, a teacher, and his wife, Morenike (nee Olukoya), who ran a business selling organic fruit. Early on he was “neglectful” of his studies, but his father helped him through a bad period at school and he completed a degree in medical sciences at the University of Ibadan.

He later graduated in medicine from Birmingham University in 1979 before returning to Ibadan as a professor in 1980. He was appointed provost of the university in 1990.

When, in the 2000s, the HIV/Aids crisis loomed large in Nigeria, Osotimehin became concerned with reducing transmission and – mindful that 58% of Nigerian HIV sufferers were women – took on roles as director general of the Nigerian National Agency for the Control of Aids and chairman of the National Action Committee on Aids. He also became, from 2002 to 2008, project manager of a World Bank-assisted HIV/Aids programme in Nigeria that helped the government to increase the number of Nigerian people on antiretroviral treatment to 250,000. Despite relative success, he said in an interview with the Guardian that the focus on HIV/Aids had “cost family planning a decade” – a remark that proved controversial with others involved in global health.

From 2008 to 2010 he was minister of health in President Goodluck Jonathan’s cabinet, a post in which he helped to upgrade Nigeria’s medical system by ensuring that 15% of the national budget was allocated to healthcare. He also had success in creating Nigeria’s first overall primary healthcare plan, which managed to impose some sort of order across the differing ideologies of the country’s 36 states.

In 1973, he married Olufunke Olukoya. She survives him, along with their son, four daughters and four grandchildren.

• Babatunde Osotimehin, doctor and public health administrator, born 6 February 1949; died 4 June 2017