The Neptis Foundation determines the direction and content of its research and publication program, in accordance with priorities for applying research to urban regional policy formation. It identifies specific projects and for each, it develops a series of research questions to be addressed in the project. It then identifies and contracts experienced researchers to carry out the research.

One of the first actions is to refine, with the researchers, the list of research questions, the research schedule, and products. Neptis comments upon drafts of studies, and the degree to which they address the research questions, but it does not determine the outcome of independent research. Final drafts are normally the subject of peer review, and these opinions are addressed by the researchers. Publication is managed directly by Neptis, although some work may be co-published with academic presses.

Neptis does not accept unsolicited requests for financial support of research.