This study aimed to demonstrate the pharmacological efficacy of mitochondrial dynamics modulators, including the fission inhibitor Mdivi-1 and the fusion promoter M1, on parameters in brain and cognitive performance in rats with iron overload condition. Forty male Wistar rats were randomly categorized into two groups to receive either 10% dextrose in normal saline (control, n = 8) or iron dextran (100 mg/kg, Fe group, n = 32) via intraperitoneal injection for six weeks. During the fifth week of injection, rats in the Fe group were further categorized into four groups (n = 8 each) to subcutaneously injected with 1) vehicle (10% DMSO in normal saline), 2) deferoxamine (DFO) (25 mg/kg), 3) Mdivi-1 (1.2 mg/kg), or 4) M1 (2 mg/kg) for further two weeks. Behavioral tests, such as novel object recognition and Morris water maze, were performed post-treatment. Non-heme iron levels in plasma and parameters in the brain, including tight junction-related blood-brain barrier proteins, lipocalin-2, iron levels, ferroptosis, inflammation, mitochondrial function, dynamics, mitophagy, and Alzheimer-like proteins, were assessed. DFO mitigated iron overload condition and brain abnormalities, partially ameliorating cognitive decline. Mdivi-1 and M1 showed superior effects by preventing brain inflammation, LCN2 elevation, and mitochondrial dysfunction, restoring memory function (hippocampal-dependent manner) and spatial cognition (recognition manner). These findings indicate that modulating mitochondrial dynamics via fission inhibitor and fusion promoter could be promising novel pharmacological interventions for the brain in iron overload condition.