RIKEN's campus at Wako, on the outskirts of Tokyo, is the second largest of the five institutes and is also the location of the administrative headquarters for the entire organization. The Wako campus facilities also include two cafeterias and three cafes, eight subsidized apartment buildings, a barbershop, a bookstore, convenience stores, a library, a nursery providing monthly daycare, two permanent exhibitions, and a clinic. There are also tennis courts, badminton courts, and an all-purpose field for use by employees.

The RIKEN headquarters at Wako manages the whole of RIKEN. Included within it are a variety of administrative sections including the Office of the President, the Committee for Research Strategy, the Public Relations Office, and the Global Relations Office, which provides support in various aspects of life to foreign scientists and their families (and organized the creation of this website). The HQ also encompasses the Advanced Center for Computing and Communication (ACCC), the Next Generation Supercomputer Center, the XFEL Project Head Office, and the Planning Office for the Institute for Computational Science, and oversees RIKEN's overseas offices in Singapore and China (see below).

The Wako Institute comprises three research centers: the Advanced Science Institute (ASI), the Brain Science Institute (BSI), and the Nishina Center for Accelerator-Based Science. The Nishina Center incorporates the RI Beam Factory (RIBF) which includes within it a Ring Cyclotron (RRC) and Superconducting Ring Cyclotron (SRC). (The RIKEN BNL Research Center at Brookhaven National Laboratory and the RIKEN-RAL Muon Facility at the Rutherford Appleton Laboratory in the U.K. are administratively a part of the Nishina Center).

Research Cluster for Innovation

The RIKEN Research Cluster for Innovation, also located at Wako campus, includes the RIKEN Innovation Center, the RIKEN Program for Drug Discovery and Medical Technology Platforms, the RIKEN Biomass Engineering Program and the Computational Science Research Program.

Located in Tsurumi Ward at the northern edge of Yokohama city, the Yokohama Institute is one of RIKEN's larger institutes, with a staff of more than 1,000 employees. The Yokohama Institute is home to the Plant Science Center, the Center for Genomic Medicine, the Research Center for Allergy and Immunology, the Omics Science Center, the Systems and Structural Biology Center, the Bioinformatics and Systems Engineering Division, and the Genomic Sciences Research Complex, and, serves as the administrative arm of the Center of Research Network for Infectious Diseases.

The Institute's NMR Facility on the Yokohama campus has 40 high performance NMR devices used for analysis of protein structure and function, the largest collection of its kind in the world, and is also open to use by academic and corporate researchers. The unusual architecture of the Yokohama Institute's West NMR complex, whose cluster of silver huts has been described variously as hanging bells, little shrines, Mongolian yurts, and even space stations, won third prize in a local architecture competition.

The Yokohama Institute also has administrative sections specific to the Yokohama campus under the Yokohama Institute Research Promotion Division, as well as a day-care facility, a cafeteria, a library room, and a multipurpose space for seminars that can also be reserved for badminton, yoga and aerobics or similar recreational activities. There is also a public indoor swimming facility called Fureyu located just a 10-minute walk away.

First opened in October 1984 to promote gene research, RIKEN's Tsukuba Institute is situated in Ibaraki Prefecture one hour northeast of Tokyo, and is organized around its BioResource Center, established in January 2001. Activities at the BioResource Center focus on the collection, preservation and distribution of biological material for experiments including genes, cultured cells and living organisms, and on providing training and education for the handling of bioresources.

Aside from the BioResource Center, the Tsukuba Institute also houses two collaborative groups, the Ishii Research Collaborative Group and the Shinozaki Research Collaborative Group. Facilities include a cafeteria, a dual-purpose outdoor court with night lights for volleyball and tennis and a rooftop garden.

Of all RIKEN's institutes, the Harima Institute is by far the largest in terms of its physical size, measuring a total of 1.41 square kilometers or roughly the equivalent of two 18-hole golf courses.

Based in Harima Science Park City west of Kobe, Hyogo Prefecture, the Harima Institute was established in October 1997 when the Super Photon Ring-8 (SPring-8), the world's largest synchrotron radiation facility, was first opened to the public. SPring-8 was built over a period of six years between 1991 and 1997; the Harima Institute was established to manage the campus where SPring-8 is located and to provide general support for synchrotron radiation research using SPring-8.

The RIKEN SPring-8 Center was created in October 2005 within the Harima Institute to support RIKEN’s own synchrotron radiation research, which has expanded to include the development of an XFEL (X-ray Free Electron Laser) facility for the creation of X-ray laser beams, to be completed in 2010. Use of SPring-8 (as well as XFEL once it is completed) is shared with universities, industry and other institutions.

Located on an artificial island of reclaimed land in Kobe Bay, RIKEN's Kobe Institute was established in April 2002 as an organizational framework for the Center for Developmental Biology (CDB), and is the smallest of all of RIKEN's five institutes, measuring a total area of 18,661 m2. In April 2007, the Kobe Institute added the Molecular Imaging Research Program (MIRP), later renamed the Center for Molecular Imaging Science (CMIS) in October 2008. In April 2011, the RIKEN Quantitative Biology Center (QBiC) was established to study the complex spatiotemporal relationships that exist between individual elements of biological systems. The Kobe Institute also added the High Performance Computing Infrastructure (HPCI) in 2011.

The Kobe Institute has its own administrative Research Promotion Division. There is a cafeteria for employees, and thanks to the cooperation of Kobe City, two tennis courts with lighting for night use.

Advanced Institute for Computational Science

The Kobe Institute houses the  Advanced Institute for Computational Science (AICS), established in Kobe on July 1, 2010. This new addition to the RIKEN organization is responsible for operating the Next-Generation Supercomputer, or “K” computer, which was recently named the fastest computer in the world.