The origins of industrial ecology trace back to at least the late 18th century and to Thomas Malthus’ study of the relationship between population growth and economic output. The literature developed in various ways during the next two centuries, notably including the Tragedy of the Commons, Spaceship Earth, The Limits to Growth, and Sustainable Development.

In 1989, Scientific American published what would prove to be a seminal article for the field of industrial ecology. The article by Robert Frosch and Nicholas Gallopoulos was titled “Strategies for Manufacturing” and suggested the need for "an industrial ecosystem" in which "the use of energies and materials is optimized, wastes and pollution are minimized, and there is an economically viable role for every product of a manufacturing process".

Frosch and Gallopoulos envisioned a more integrated model of industrial activity that would be environmentally sustainable on a global level. Their article was the catalyst for a Symposium held by the US National Academy of Sciences in the early 1990s that has been heralded as a founding event for the modern field of industrial ecology. At around this time, Graedel and Allenby published their seminal definition of industrial ecology:

“Industrial ecology is the means by which humanity can deliberately and rationally approach and maintain sustainability, given continued economic, cultural, and technological evolution. The concept requires that an industrial ecosystem be viewed not in isolation from its surrounding system, but in concert with them. It is a systems view in which one seeks to optimize the total materials cycle from virgin material, to finished material, to component, to product, to obsolete product, and to ultimate disposal. Factors to be optimized are resources, energy and capital.”

During the decade following the symposium, the US-based effort becoming known as industrial ecology joined with and built upon a substantial body of research, practice, and expertise already underway throughout the world, but especially in northern Europe. The field’s growth was signaled by two Gordon Research Conferences in the United States as well as a number of special sessions at annual meetings and conferences of various professional and scientific organizations.

In the late 1990s the field gained increased international recognition through the creation of the Journal of Industrial Ecology - now a widely respected, scholarly, peer-reviewed journal. The journal is based at the Center for Industrial Ecology at Yale University and is edited in collaboration with the Norwegian University of Science and Technology (NTNU) and Tsinghua University.

In 2003, NTNU offered the first PhD program in Industrial Ecology, followed by a masters program the year after. In 2005, Leiden University and Delft University of Technology started offering a joint MSc degree in Industrial Ecology. Across the globe, industrial ecology is currently taught through individual courses or specializations, often within engineering programs or interdisciplinary degrees that focus on the environment.

In the 2010s, the circular economy became a leading concept in academic, industrial, and policy circles. The circular economy embodies many of the approaches and findings of industrial ecology, including its life cycle perspective, focus on closed-loop systems, design for the environment, and industrial symbiosis. Many circular economy efforts are supported or created by leading industrial ecologists. Moreover, circular economy businesses and other initiatives often employ graduates from industrial ecology programs.