Alzheimer’s disease (AD) is the most prevalent ageing-associated neurodegenerative disease. Deep brain stimulation is a novel therapeutic approach, but long-term effects remain unknown. We previously demonstrated that acute intracranial self-stimulation (ICSS) in medial forebrain bundle (MFB) improves the acquisition but not 72-hour retention of a spatial learning task and regulates expression of specific miRNAs in a rat AD model. This study aims to analyse the effect of a chronic MFB-ICSS treatment on spatial memory and miRNA serum expression levels in a rat AD model by streptozotocin (STZ) injection. Rats were implanted with the electrode and injected 2 mg/kg STZ or vehicle into ventricles. MORRIS tests were performed at 40 days and 4.5 months post-STZ. Between the two tests, STZ rats received ICSS for 13 weeks (one session/week) or sham treatment. Serum levels of miRNAs were quantified by qRT-PCR at 40 days (S0) and 2 (S1) and 4.5 months (S2) post-STZ. Our results indicate that at 4.5 months STZ+ICSS rats showed better acquisition and retention of the Morris task than STZ-sham rats. At 40 days, miR-30c and miR-16 were significantly upregulated in STZ group and decreased from S0 to S1 in both STZ-sham and STZ-ICSS group. However, levels of miR-495 in the STZ-sham group followed a significant increase from S1 to S2 that is not observed in control and STZ+ICSS groups. This study reveals a protective effect of ICSS-MFB on spatial memory dysfunction after STZ and differential serum changes of the miRNAs, supporting their use as progression biomarkers.