Accumulation of evidence suggested the involvement of autophagic pathways and their associated AktmTOR (mammalian target of rapamycin) signalling cascade in the pathogenesis of autism spectrum disorder (ASD). Histamine 3 receptors antagonism may be neuroprotective in ASD, as this antagonism modulates autophagy which is reported to be impaired in ASD. Therefore, the effects the novel H3 receptor antagonist E169 (2.5, 5, and 10 mg/kg, i.p.) on short-term memory (STM), long-term memory (LTM), and anxiety level in male Black and Tan BRachyury (BTBR) mice were evaluated using Novel object recognition test (NORT) and open field locomotor (OFT) tests respectively. In NORT, E169 (2.5 mg/kg, i.p.) significantly improved the memory of tested BTBR mice, and the effects of E169 were similar to those of the reference mTOR inhibitor rapamycin, and were reversed following co-administration with the centrally penetrant H3 receptor agonist (R)-α-methylhistamine (RAMH). Furthermore, E169 enhanced the BTBR memory by inhibiting H3 receptors and regulating the extent of disruption in the expression of cerebellar Akt, mTOR, and LC-3 proteins of treated mice. Moreover, E169 (2.5 mg/kg, i.p.) restored the disturbed anxiety levels and hyperactivity observed in OFT. In summary, the findings indicate that H3 receptor antagonists like E169 could play a role in simultaneously regulating disrupted brain neurotransmitters and the dysregulated cerebellar Akt-mTOR signaling pathway associated with autophagy in neurological diseases. Therefore, activation of cerebellar autophagy represented by H3 receptor antagonist E169 may serve as an effective pharmacological therapeutic target for the ASD-like behavioral phenotypes and may add new therapeutic management strategy for the multifactorial disorder ASD.