Poly-arginine peptides are a promising class of bioactive compounds that are capable of crossing the blood-brain barrier (BBB) and present neuroprotective properties. In this study, we test the activity of poly-arginine peptides in a triple-transgenic mouse model of Alzheimer’s disease. To identify the best candidate, we examined the relative neuroprotective efficacy of the compounds with various lengths (R7, R9, and R11) via assessment of memory acquisition, long-term hippocampal potentiation (LTP), and cytotoxicity. Also, we explored the expression profiles of hundreds of key cell signaling proteins, and perform a high content antibody microarray comparative analysis of brain samples. The chronically treated animals with poly-arginine R9 show significantly improved acquisition of memory. This compound rescues hippocampal LTP deteriorated by Aβ at a better rate than other agents tested in this study and induces cellular pathways involved in neuroprotection and neuroplasticity. The treatment escalates the expression levels of Synapsin Ia in the mice hippocampi; however, it has no significant effect upon the rate of beta-amyloidosis. Poly-arginine R9 peptide is a well-tolerated compound that crosses the BBB and presents unique neuroprotective qualities. The substance halters the development of AD symptoms in a murine model and can be recommended for clinical investigation.