By the mid-1950s, the Western world had CERN, established near Geneva in 1954 as a collaborative European laboratory for nuclear research. The socialist bloc wanted its own. On 26 March 1956, representatives of eleven countries signed the founding agreement in Moscow. The USSR contributed 50 percent of the budget, the People's Republic of China 20 percent, and the remaining nations made up the rest. The institute was built on the foundation of two existing Soviet facilities: the Institute of Nuclear Problems, which had operated a synchrocyclotron at Dubna since the late 1940s, and the Electrophysics Laboratory, where Academician Vladimir Veksler was constructing a proton synchrophasotron with a then-record energy of 10 GeV. By February 1957, the United Nations had registered JINR as an international organization. Its first director was Dmitry Blokhintsev, the physicist who had just completed the world's first nuclear power plant at Obninsk.

The institute's research power comes from its accelerators and reactors. The principal instrument is a nuclotron, a superconductive particle accelerator that pushes particles to energies of 7 GeV. Three isochronous cyclotrons operate at 120, 145, and 650 MeV, alongside a phasitron at 680 MeV and the original synchrophasotron at 4 GeV. A neutron fast-pulse reactor capable of 1,500-megawatt pulses serves nineteen separate experimental stations. Eight laboratories specialize across the full spectrum of nuclear science: theoretical physics, particle physics, heavy ion physics, condensed matter, nuclear reactions, neutron physics, radiobiology, and information technology. Some 5,500 staff members work here, including 1,200 researchers holding over 1,000 Ph.D.s from eighteen countries.

JINR's most visible legacy is written in the periodic table itself. The Flerov Laboratory of Nuclear Reactions, named after physicist Georgy Flyorov, has been the epicenter of superheavy element synthesis for decades. Element 114, flerovium, was synthesized in 1999. Element 116, livermorium, followed in 2000. Oganesson, element 118, came in 2002. Elements 115 (moscovium) and 113 (nihonium) were identified in 2003, and tennessine, element 117, was synthesized in 2010. The Superheavy Element Factory, opened in 2019, represents the next generation of this work: a facility capable of beam intensities ten times greater than previous equipment, designed to probe the reactions needed to create elements 119 and 120, which would open an entirely new row of the periodic table. Bruno Pontecorvo's 1957 prediction of neutrino oscillation, published while he worked at JINR, stands as another landmark in the institute's scientific output.

The politics of international science have buffeted JINR since its founding. China was a major contributor in 1956 but later withdrew. North Korea was a founding member, suspended since 2015. In December 2022, following Russia's invasion of Ukraine, the Czech Republic, Poland, and Ukraine terminated their memberships, while Bulgaria and Slovakia suspended participation. CERN, with which JINR had collaborated since 2014, imposed restrictions and signaled a review of the relationship. As of early 2023, thirteen member states remain active, with associate members including Germany, Hungary, Italy, South Africa, and Serbia. The institute's cooperation with UNESCO, ongoing since 1997, continues. The shifting membership reflects a tension that has followed JINR throughout its existence: the science is genuinely international, but the politics of the host country are not always compatible with the principles of open collaboration.