The Max Planck Institute for Human Cognitive and Brain Sciences at Leipziger Stephanstraße in Leipzig was established on 1 January 2004 by a merger between the former Leipzig Max Planck Institute of Cognitive NeuroScience and the Munich Max Planck Institute for Psychological Research. Following a two-year transitional period that set the stage for the joint Institute's future research whilst simultaneously allowing ongoing projects at each branch to be continued, the Munich institute moved to Leipzig in late 2006.

The Leipzig Max Planck Institute of Cognitive NeuroScience was established on 1 October 1994 and was inaugurated on 12 September 1995. Until completion of the new institute building, it was located in the former premises of the Reclam publishing house Leipzig's Inselstrasse. The two scientific departments within the Institute were led by the two founding directors Professor Angela D. Friederici (Neuropsychology) and Professor D. Yves von Cramon (Neurology).

The former Max Planck Institute of Psychological Research, which provided the second strand of today’s Institute, was established in 1981 at Amalienstrasse 33 in Munich. The former Institute's building now hosts the Max Planck Institute for Foreign and International Social Law as well as the Max Planck Digital Library. Founding director Professor Franz Emanuel Weinert headed the Department of Developmental Psychology, which gained an international reputation through its eminent research into the development of cognitive abilities of children and youth. From 1990, a second department, headed by Professor Wolfgang Prinz, focused on cognitive psychology and examined the cognitive bases of perception and action.

On 5 June 2003, the Senate of the Max Planck Society decided to merge both MPIs into the Max Planck Institute for Human Cognitive and Brain Sciences. Building works for the annexe to the existing building of the MPI on a plot adjoining the Institute started in 2005; at the end of 2006, the period of transition and relocation of the former Munich Institute to Leipzig was completed. Work at the Institute is organized in departments and independent research groups. Heading the departments are directors with permanent contracts, who are independent in their research activities. Employment on the independent research group level is limited to five years and aimed at giving young scientists a head start in their careers. The Institute employs about 200 staff members.

Research focuses upon neurological bases of the higher functions of the human brain, with particular emphasis on the connection between brain processes and cognition, behaviour, and action. Specific research topics investigate how humans plan and produce language and action, the way in which they perceive actions and action effects, as well as language and music. The main research focus is on the interaction and common functional bases of production and perception in these and other cognitive domains. Methods applied at the Institute investigate brain activities during language and music communication as well as during action planning and execution. A significant condition for part of the research at the Institute – and unique within Germany – is the collaboration with the Day Clinic for Cognitive Neurology headed by Professor Arno Villringer, director of the Department of Cognitive Neurology. The MPI for Human Cognitive and Brain Sciences now consists of four departments; a fifth department will be called into life in the near future:

Research staff in the departments and independent research groups come from the most diverse backgrounds - there are physicists, philosophers, biologists, linguists, psychologists, mathematicians, computer scientists, and medical experts. There can be no alternative to this interdisciplinary approach, as experimentation with image generating methods requires that data be correctly read and interpreted, with new findings mostly resulting from daily routines such as the analysis of video signals with the aid of complex computational models. Those who join the Institute can expect to work in a team of excellent scientists using advanced equipment and approved methods and expertise. The library provides access to 325 periodicals and altogether over 16,000 media units.
In 2005, construction of an annexe on the plot adjoining the Institute commenced. This building was inaugurated in 2008 and provides an optimum research environment for the approximately 200 employees working at the Institute. A section of the annexe houses the Institute’s 7 Tesla scanner and was opened prior to the main annexe in summer 2007.