From 1991–1994 Haeberle was a visiting professor at Humboldt University and from 1994–2001 he was founder and director of the Archive of Sexology at the Robert Koch Institute. After his retirement from government service in 2001, he continued his work privately as director of the Magnus Hirschfeld Archive for Sexology, which he financed himself and which ran on the server of Humboldt University.
In January 2003, he put the world's first freely accessible course (MOOC) online. In 2004 he presented it in Beijing's Great Hall of the People. Subsequently, it was, together with other courses, translated into Chinese. Today, an entire "open access" curriculum of 6 courses (6 Semesters)on sexual health is available in 7 languages: English, Spanish, Portuguese, Chinese (both simplified and traditional), Russian, Czech, and Hungarian. Haeberle's online Archive now offers sexual health information in a total of 15 languages. In July 2013 he left the server of Humboldt University and continued on a private server of his own as Director of his still personally funded Archive for Sexology. Since October 2009, his print library and collections have been available as Haeberle-Hirschfeld Archive at the central library of Humboldt-University In 2005, he joined the University of Hong Kong as an honorary professor, first at the Faculty of Medicine, then at the Family Institute. From 1986–2002 he was president of the German Society for Social-Scientific Sexuality Research.