Ernst Homburg was born in Venlo, the Netherlands, on 2 August 1952.
From 1964 to 1969 he was educated at the Protestant Lyceum (nowadays Huygens Lyceum), Eindhoven. From 1969 to 1978 Homburg studied chemistry at the Free University Amsterdam and at the University of Amsterdam. At the Free University he followed a course in the History of Science by Professor Reijer Hooykaas, one of the Dutch pioneers in this field. Homburg wrote a thesis on the Disproportionation of Propene.
In 1978 and 1979 he worked at the Department of Pharmacy of the University of Groningen and from 1979 to 1983 he was research fellow in the History of Science in the Chemistry Department of the University of Nijmegen. Here he worked on a study of the development of the dye industry, supervised by Willem J. Hornix. From 1984 to 1993 he was assistant professor for Chemistry and Society at the same department. In the period from 1989 to 1993 he was also a part-time assistant professor for History of Technology in the Department of Philosophy and Social Sciences of the Technical University Eindhoven. 
In 1993 he received his Doctorate in History at the University of Nijmegen with a dissertation entitled Van beroep "Chemiker": De opkomst van de industriële chemicus en het polytechnische onderwijs in Duitsland, 1790-1850 ("Chemiker" by occupation : the rise of the industrial chemist and polytechnic education in Germany, 1790-1850). His supervisor was dr. P.M.M. (Paul) Klep (Professor of Economic and Social History). 
From 1993 to 2001 Homburg became assistant professor History of Technology in the Department of History of the Faculty of Arts and Sciences of Maastricht University. This period was followed by a full professorate at the same institute on a chair endowed by the Dutch Stichting Historie der Techniek (SHT) (Foundation for the History of Technology).
In August 2018 he retired.