Straight out of INSEAD, Dougier was recruited by Shell International and worked for the company in Paris and London from 1963 to 1969, including in marketing. He then joined the Expansion business press group from 1969 to 1974, working with Jean-Louis Servan-Schreiber, with whom he created the monthly magazine Le Management. In partnership with INSEAD he also started an English language quarterly, European Business.
The events of May 1968 in Paris marked him deeply and pushed him towards questions about how society was changing. In 1975, with financial support from Christian de Bartillat of Éditions Stock, he launched Autrement, a quarterly review of social, cultural and political change. The review found its readers quickly and in 1983 became a full publishing house, Éditions Autrement. It grew to almost 40 collections across the humanities, literature and children's books, among them Monde (1983), Morales, Mémoires, Mutations and Mook, with more than 2,500 titles published between 1975 and 2011.
In 1993 Autrement launched a literature list with works by Laurie Colwin, Joseph Conrad, Kenneth Cook, Eduardo Mallea, Grazia Deledda and Margaret Atwood. Its French edition of Address Unknown by Kathrine Kressmann Taylor, published in 1999, became a bestseller and passed a million copies. The same year, 1993, saw the first children's picture book collection, later joined by the documentary series Junior and the wordless Histoire sans paroles, and the first of the house's atlases, Atlas/Monde, followed by atlases of memory, of wars and of megacities. Dougier also discovered the novelist Gaëlle Josse, whose early novels appeared at Autrement.
Autrement passed to the Flammarion group, already its distributor since 2008, in a sale announced in March 2010 and completed in 2011. Dougier kept the presidency for a time before gradually stepping back.
Throughout these years he ran parallel ventures in social innovation. From 1975 his Atelier pour la création et l'expérimentation sociale held seminars and field studies with partners in the social economy. From 1979 to 1985 he organised the annual Ateliers d'octobre for social entrepreneurs, and later the Trans-européennes de littérature and young creators' days. In 1981 he devised the boutiques de gestion, advice centres for budding entrepreneurs, opening the first one in Autrement's own offices with help from the European Social Fund; the network later spread across France.
In 2014, aged 78, he founded the Ateliers Henry Dougier, an independent structure for experimental publishing, and also set up the Fondation R. Its first collection, Lignes de vie d'un peuple, launched in September 2014, described the real life of countries, regions and diasporas through testimonies gathered by local authors, each cover showing a mapped hand of an inhabitant. Later series included Métamorphoses d'une nation (2016), a literature list opened in 2017 with Gaëlle Josse's Un été à quatre mains, and Le roman d'un chef-d'oeuvre (2021). The Ateliers also produced folded graphic journals written by young people from working class neighbourhoods. In September 2025 he handed the presidency to Maureen Demidoff and the house became Ateliers HD.