Henk Jan Bakker was born 6 December 1964 in the village of Marssum in the northern province of Friesland in the Netherlands, and raised in Gouda. He studied Political Science (International Relations) at Leiden University, where he graduated in 1991.

In 1992 he joined the Ministry of Foreign Affairs. After a 3 year period at the United Nations Department of the Ministry, he was posted to the Netherlands embassy in South Africa in 1995 as deputy head of development cooperation.

In 1998 he returned to the Netherlands, to be seconded to the Ministry of Economic Affairs where he became responsible for Dutch bilateral economic relations with China. In 2001 he returned to Foreign Affairs for a one year posting at the human rights department.

He was subsequently posted as economic counsellor at the Netherlands Permanent Representation to the OECD in Paris, where in 2004 he was elected chairman of the Working Party of the Trade Committee.

In 2006 he was appointed head of the economic division at the Netherlands embassy in London.

In 2010 he returned to the Netherlands to become head of business environment in the Department for Sustainable Economic Development at the MFA. A year later he was appointed Deputy Director for Human Resources.

From 2014 to 2016 Henk Jan Bakker was Ambassador to Afghanistan, and from 2016 until 2020 Ambassador to Uganda.

Since August 2020 he is ambassador of the Netherlands to Ethiopia and Djibouti, and Permanent Representative to the African Union, IGAD and UNECA.