Chemotherapy-related cognitive impairment (CRCI) significantly impacts cancer survivors. Due to unclear mechanisms, effective treatments for cognitive deficits are lacking. Here, we examined if microglia-mediated deficits in synaptic plasticity drive CRCI. Adult male mice were treated with the chemotherapeutic drugs 5-fluorouracil and leucovorin (5-Fu/LV, intraperitoneal injection, I.P.) on Days 1, 8, and 15 at a dosage of 50 mg/kg for 5-Fu and 90 mg/kg for LV for 3 weeks. Cognitive function was assessed using a novel object recognition (NOR) test 4 weeks after completion of 5-Fu/LV treatment. Compared with vehicle treatment, 5-Fu/LV treatment reduced the preference for exploring novel objects in the NOR test. Treatment with 5-Fu/LV increased the numbers of Iba1-positive microglial and CD68-positive/Iba1-positive microglia with shortened process lengths and diminished endpoints but decreased the number of phagocytotic (≤ 1 FITC-labeled beads) Iba1-positive microglia. Furthermore, 5-Fu/LV treatment reduced the long-term potentiation (LTP) recorded in the hippocampal CA1 region in response to a theta burst stimulation of the CA3-CA1 pathway and decreased the evoked N-methyl-D-aspartic acid receptor (NMDAR)-excitatory postsynaptic currents (NMDAR-EPSCs) in CA1 neurons. Cotreatment with the microglial inhibitor minocycline (33 mg/kg, daily for 3 weeks) restored cognitive deficits and microglial ramification, decreased the number of CD68-positive microglia, and reversed the reductions in LTP and the amplitude of NMDAR-EPSCs in 5-Fu/LV-treated mice. Our data suggest that microglial dysfunction and related synaptic dysfunction contribute to 5-Fu/LV-induced cognitive impairment.