Background: Our recent studies show that transplants of intestine epithelial stem cells (IESCs) promote acute and long term recovery after stroke in middle-aged rats. To improve the translational potential of this therapy, we investigated whether injections of the IESC conditioned media (CM) would be similarly effective in improving acute and chronic stroke outcomes. Methods: Conditioned media was collected intestinal organoids culture from young animals and processed for proteomic and tropic factors analysis. CM efficacy was tested in middle-aged male and female rats assigned to the following groups: Control (sham), stroke+vehicle injection, or stroke+IESC-CM treatment. Middle cerebral artery occlusion (MCAo) was induced by Endothelin-1 (vasoconstrictor). Conditioned media was injected ip (CMip) 4h/24h/48h after stroke. In the acute phase, infarct volume, sensorimotor function and serum levels of the gut permeability markers were measured 4d post stroke. Long term (4 weeks after stroke) depressive-like behavior was assessed by the Social Interaction test, and cognitive performance by the Novel object Recognition test and Barnes maze test. Results: Proteomic analysis of CM showed elevated levels of small peptide growth factors ad large matrix molecules. IESC-CMip treatment significantly improved acute stroke outcomes and reduced gut permeability in middle-aged hosts of either sex. In long term study, vehicle-treated MCAo animals showed depressive-like behaviors compared to their pre-stroke behaviors. In contrast, stroke animals that received IESC secretome were no different from their pre stroke performance and were similar sham (no-stroke) animals. In cognition assesments. MCAo+vehicle animals showed poor ability to discriminate the novel object and displayed impaired learning and recall on the Barnes maze. MCAo animals that received IESC secretome did not show significant improved during the Barnes learning trials, but retrieval (memory recall) performance was improved and significantly different from the vehicle group. Conclusion: Overall, these data show that IESC secretome derived from a healthy young animal can significantly improve acute stroke outcomes and specific aspects of cognitive performance.