Stroke remains a leading cause of death and disability in the world whereas limited therapies are available to restrict brain damage or improve functional recovery after cerebral ischemia. A promising strategy currently under investigation is the promotion of brain-derived neurotrophic factor (BDNF)-signalling through tropomyosin-related kinase B (TrkB) receptors, a pathway essential for neuronal survival and function. However, TrkB and BDNF-signalling are impaired in excitotoxicity, a primary pathological process in stroke also associated to neurodegenerative diseases. Pathological imbalance of TrkB isoforms is critical to neurodegeneration and is caused by calpain-processing of BDNF high affinity full-length receptor (TrkB-FL) and inversion of the transcriptional pattern of the Ntrk2 gene, which favours expression of the truncated isoform TrkB-T1 over TrkB-FL. We report here that both TrkB-FL and neuronal TrkB-T1 also undergo ectodomain shedding by metalloproteinases activated after ischemic injury or excitotoxic damage of cortical neurons. Subsequently, the remaining membrane-bound C-terminal fragments (CTFs) are cleaved by γ-secretases within the transmembrane region, releasing their intracellular domains (ICDs) into the cytosol.Therefore, we identify TrkB-FL and TrkB-T1 as new substrates of regulated intramembrane proteolysis (RIP), a mechanism that highly contributes to TrkB-T1 regulation in ischemia but is minor for TrkB-FL which is mainly processed by calpain. However, since the secreted TrkB ectodomain acts as a BDNF-scavenger and significantly alters BDNF/TrkB-signalling, the mechanism of RIP could contribute to neuronal death in excitotoxicity. These results are highly relevant since they reveal new targets for the rational design of therapies to treat stroke and other pathologies with an excitotoxic component.