The foundation of the BCCN Göttingen in 2004 is based on an initiative of the Federal Ministry of Education and Research (BMBF) to create a "Bernstein Network Computational Neuroscience" as a general framework for establishing the research area “computational neuroscience” in Germany. The aim was to structurally interconnect and to develop regional capacities and knowledge in the field of computational neuroscience and to bundle expertise in theoretical and experimental neurosciences.
Whereas the Bernstein Centers for Computational Neuroscience are the core elements from the very beginning, the BMBF launched multiple Bernstein funding lines (e.g. Bernstein Collaborations, Bernstein Award, Bernstein Focus) over the past years. Hence, the network constantly expanded not only area-wise, but also the spectrum of research methods and themes broadened.

Founded in 2007, in the Bernstein Focus Neurotechnology (BFNT) Göttingen engineers and theoreticians with a long-standing involvement in neuroscience collaborated with advanced experimental groups in order to investigate and design complete Neuro-Bionic Closed-Loop Systems, neuro-sensing and neuro-stimulation strategies. Biomedical experiments were combined with mathematical models and computational simulation pioneering to novel insights and technological applications such as legged robots and neural prostheses.

In close collaboration with industry partners (Otto Bock HealthCare GmbH, LEICA Microsystems GmbH, MED-EL GmbH, and Thomas Recording GmbH) research groups of the Göttingen Campus, the Max Planck Institute for Biophysics in Frankfurt am Main, and Hannover Medical School defined the scientific and technological core of the joint research initiative.

Coordinator of the BFNT Göttingen was Prof. Florentin Wörgötter. His chair in Computational Neuroscience at the University of Göttingen emerged from the BCCN Göttingen in 2005.

The BMBF funding enabled to create another three new chairs at the University of Göttingen: one in Systems Neuroscience (staffed with Prof. Siegrid Löwel in 2010), one in Sensorimotor Neurosciences and Neuroprosthetics (staffed with Prof. Alexander Gail in 2012) and one in Neuroinformatics (staffed with Prof. Dario Farina in 2010).

Further BMBF funding at the Göttingen Campus involved the Bernstein Focus Neuronal Basis of Learning, Bernstein Partner Collaborations, and a German-US-Collaboration.

In the first 14 years, the Bernstein partners Göttingen received a financial support by the BMBF of more than 30 Mio. € from approximately 170 Mio. € throughout Germany. Since 2018, the BCCN Göttingen is supported by the University of Göttingen, the University Medical Center, the Max Planck Institute for Dynamics and Self-Organization, the Max Planck Institute for Experimental Medicine, and the newly founded Campus Institute for Dynamics of Biological Networks.