Research projects at Rekihaku are organized and conducted with researchers in Japan and overseas. Collaborative research consists of "principal research" aiming for interdisciplinary collaboration on core research themes based on Rekihaku's mission, "fundamental research" addressing the development of methodological foundations for historical studies, and "developmental research" aimed at breaking ground for new areas of study and developing human resources.
NIHU Transdisciplinary Projects are research projects promoted by the National Institutes for the Humanities (NIHU). NIHU consists of six inter-university research institutes including Rekihaku and the following: National Institute of Japanese Literature (NIJL); National Institute for Japanese Language and Linguistics (NINJAL); International Research Center for Japanese Studies (Nichibunken); Research Institute for Humanity and Nature (RIHN); National Museum of Ethnology (Minpaku).