The institute was founded in 2002 as a non-governmental research organization. It has involved scientists who have had extensive experience in research activities in former Soviet institutes. It was a known fact that among former Soviet republics, Armenia was especially distinguished by achievements in physics, both in fundamental and applied researches. After the collapse of the Soviet Union,  practically all experiments in physics were suspended, the Armenian Accelerator, ARUS,  was shut down. However, Armenian researchers have maintained solid scientific traditions, especially in the field of theoretical particle and high energy physics. ITPM has attracted researchers who intended to do independent research activities. The circumstance that the institute is a non-governmental organization allows for free and flexible planning of research studies. On the other hand, the structure of the institute allows for flexible collaboration with engineers.  A few years later, this has resulted in the creation of а new department of technology.

The ITPM is a leading research center in the field of neutrino physics not only in Armenia but also in the entire region. In 2005, the ITPM, with the support of ICTP (UNESCO) organized the first Neutrino International Conference in Armenia (NICA-2005).

ITPM has been one of the members of DUNE at the time of its creation. ITPM is also a member of JUNO and HyperKamiokande.