After working as a film script reader in Los Angeles, an aid worker in Uganda, and a research assistant and junior journalist working on human rights and the arming of Iraq by foreign powers and other matters, he became co-ordinator of the Green College Centre at Oxford University from 1992 to 1994, which focused on climate change and other environmental issues. In 1995 and 1996 he worked on Costing the Earth, the flagship environment program on BBC Radio 4.
From 1996 to 2002 he wrote on topics such as: energy, science, environment and human rights for The Financial Times, The Independent, New Scientist, The Ecologist, Environmental Finance, Green Futures (as senior correspondent) and other newspapers, magazines, and broadcast media. In 1999 he won the IUCN-Reuters award for best environmental writing in western and central Europe. From 1996 to 2002 he was also a consultant, analyst and writer for government, commercial and non-profit organisations.
From 2002 to 2005 he was a senior editor at OpenDemocracy, a project for open global politics, where he commissioned, edited and contributed to analysis and debate on globalisation, security, the environment, and the politics of climate change. He has been a contributing editor and member of the editorial advisory board at chinadialogue, and a member of the advisory group for Artists' Project Earth. He keeps an occasional blog called Grains of Sand .
His Book of Barely Imagined Beings: A 21st Century Bestiary  received the Roger Deakin Award from the Society of Authors in 2009 and the Royal Society of Literature Jerwood Award in 2010 while it was a work in progress, and was published by Granta in October 2012 and by Chicago University Press in April 2013 (ISBN 978022604470). In 2013 it was short-listed for the Royal Society Winton Prize for Science Books, for the Society of Biology book awards (general category), and for Best British Book category of the British Book Design & Production Awards.
The book covers an eclectic range of creatures whose development and variance provide an exegesis on the human condition. It orchestrates an impressive spread of literary and scientific knowledge enabling Henderson to reach his environmentalist philosophy in the context of religious and artistic endeavor. It is a dense well-written book, slow reading but thoroughly pleasurable and worthwhile.
One of his favourite sayings comes from Franz Kafka: "There is hope; but not for you". This is followed swiftly by Bertrand Russell's "only on the firm foundation of despair can the soul's habitation be safely built," leading to Henderson's own assertion of "the value of the 'little' Earth we have actually in front of us" (see Book of Barely Imagined Beings: A 21st Century Bestiary, pp. 91–96, whose conclusion finds "Evidence enough that there are miracles in life.")