Non-profit and non-governmental organizations provide additional career options for scientists and engineers, in addition to the many opportunities they offer non-researchers.

Some of these groups are similar to academia in their research-based missions [for example, the Woods Hole Oceanographic Institution (WHOI), the largest independent oceanographic institution in the world, is a private, non-profit research facility, and the Monterey Bay Aquarium Research Institute is a part-science, part-engineering institute that develops instruments, systems, and methods for scientific studies of the deep ocean and specializes in exploration with remotely operated vehicles]. Other non-profit organizations concentrate more on environmental advocacy (well-known examples include the Nature Conservancy, the World Wildlife Foundation, Greenpeace, and the Sierra Club).

A non-governmental organization (NGO) is generally defined as a nonprofit group or association organized outside of institutionalized political structures. Many NGOs have social objectives, while others serve particular constituencies. NGO activities range from research, information distribution, training, local organization, and community service to legal advocacy, lobbying for legislative change, and civil disobedience. NGOs range in size from small community groups to huge organizations with national or international memberships.

Because there are so many non-profit and non-governmental organizations, there are many choices in terms of specialty area, size, and geographic location. A concern for many in these sectors is funding pressure and competition, the relatively small number of pure research positions available, and the salaries, which tend to be lower than in industry or academia.