The underlining mechanism in neural mitochondrial dysfunction and consequences neurotoxicity, and cognitive behavior after methylphenidate (MPH) prolonged uses is unclear and proposing of therapeutic approaches for treatment of these types of neurotoxicity is one of the main goals of scientist in this manner. MPH-induced mitochondrial dysfunction in neural cells caused induction of oxidative stress, apoptosis, inflammation and cognition impairment, which leads to neurotoxicity, was reported previously but role of key neural cells proteins and involved signaling pathway in this manner remained indeterminate. Tau protein aggregation is a biomarker for mitochondrial dysfunction, neurodegenerative event and cognition impairment. Tau aggregation occur by stimulation effects of Glycogen synthase kinase-3(GSK3β) and phosphatidylinositol 3-kinase (PI3K) which activates protein kinase B(Akt) and causes inhibition of phosphorylation(activation) of GSK3β, thus Akt activation can cause inhibition of tau aggregation (hyper-phosphorylation). Management of mentioned MPH-induced mitochondrial dysfunction and consequences of neurotoxicity, and cognitive behavior through a new generation neuroprotective combination, based on modulation of disturbed in Akt function and inhibition of GSK3β and tau hyper-phosphorylation can be a prefect therapeutic interventions. Therefore, finding, introduction and development of new neuroprotective properties and explanation of their effects with potential capacity for modulation of tau hyper-phosphorylation via PI3/Akt/GSK signaling pathway is necessitated. During recent years, using new neuroprotective compounds with therapeutic probability for treatment of psychostimulant-induced mitochondrial dysfunction, neurotoxicity and cognitive malicious effects have been amazingly increased. Many previous studies have reported the neuroprotective roles of minocycline (a broad-spectrum and long-acting antibiotic) in multiple neurodegenerative events and diseases in animal model. But the role of neuroprotective effects of this agent against MPH induced mitochondrial dysfunction, neurotoxicity and cognitive malicious and also role of tau hyper-phosphorylation by modulation of PI3/Akt/GSK signaling pathway in this manner remain unknown. Thus we suggested and theorized that by using minocycline in MPH addicted subject, it would provide neuroprotection against MPH-induced mitochondrial dysfunction, neurotoxicity and cognitive malicious. Also we hypothesized that minocycline, via modulation of PI3/Akt/GSK and inhibition of tau hyper-phosphorylation, can inhibit MPH-induced mitochondrial dysfunction, neurotoxicity and cognitive malicious. In this article, we tried to discuss our hypothesis regarding the possible role of minocycline, as a powerful neuroprotective agent, and also role of tau hyper-phosphorylation related to PI3/Akt/GSK signaling pathway in treatment of MPH-induced mitochondrial dysfunction, neurotoxicity and cognitive disturbance.