The Inter-University Master's Degree in Nuclear Physics is an adaptation of the previous Nuclear Physics doctoral programme to the new regulations governing postgraduate studies relating to the teaching period and introduction to research. Following its verification, the Master's Degree in Nuclear Physics was first introduced in its current format in the 2010-2011 academic year.

It previously constituted the teaching period of the Nuclear Physics doctoral programme. This programme has been awarded the Ministerial Quality Certification since 2004. The doctoral programme originally arose as a joint programme of the Nuclear Physics research groups at five Spanish universities (Granada, Huelva, Seville, Salamanca and the Complutense University of Madrid) and two facilities of the Spanish National Research Council (Consejo Superior de Investigaciones Científicas) - the IEM in Madrid and the IFIC in Valencia. In its second academic year, the University of Santiago de Compostela also joined.. The staff participating under the programme, have extensive teaching experience and have offered doctoral courses with similar content to those presented under the doctoral programmes of each university.

The Spanish Nuclear Physics community, through the Specialist Nuclear Physics Group (GEFN) of the Royal Spanish Physics Society, has been organising the courses of the Nuclear Physics Doctoral School since 1998-99. These courses, with a weighting of three credits, were carried out at different universities and Council centres, generally over a one-week period. They were open to all interested doctoral students, mainly from Spain but also, in some cases, from overseas, and were typically attended by 10 to 15 students. These courses were included in each university's doctoral programme and were recognised as stand-alone courses by the doctoral programmes of other universities. Generally speaking, they were used by students as flexible courses.

In 1998/1999 a Nuclear Structure course and another course in Microscopic Theories were offered by the Autonomous University of Madrid. The University of Salamanca offered a course in Intermediate Energies.

In 1999/2000 the University of Seville offered a course in Nuclear Reactions and another course in Basic Nuclear Instrumentation. The CSIC – Madrid offered a course in Advanced Nuclear Instrumentation.

In 2000/2001 the Complutense University offered a course in Nuclear Structure and the University of Salamanca offered a course in Intermediate Energies.

In 2001/2002 the University of Seville offered a course in Nuclear Reactions and the CSIC-Valencia offered a course in Nuclear Instrumentation.

In 2002/2003 the CSIC-Madrid offered a course in Nuclear Instrumentation and the University of Granada offered a course in Nuclear Structure.

The initiative to convert the Nuclear Physics Doctoral School into a university doctoral programme in 2004 was therefore a logical step to consolidate a project that had been functioning successfully for various years. The quality certification and the financing it grants access to, has been essential in order to carry out this project, which requires mobility of both doctoral students and teaching staff. Following the change to the structure of postgraduate studies in 2009, the teaching aspect of the previous Nuclear Physics doctoral programme was converted naturally into the present Master's Degree course which has been offered since 2010-2011.