Status epilepticus (SE) during developmental periods can cause short- and long-term consequences to the brain. Brain damage induced by SE is associated to NMDA receptors (NMDAR)-mediated excitotoxicity. This study aimed to investigate whether blockade of GluN2B-containing NMDAR is neuroprotective against SE-induced neurodegeneration and neuroinflammation in young rats. Forty-eight Wistar rats (16 days of life) were injected with pilocarpine (60 mg/kg; i.p.) 12-18 h after LiCl (3 mEq/kg; i.p.). Fifteen minutes after pilocarpine administration, animals received i.p. injections of saline solution (0.9% NaCl; SE + SAL group), ketamine (a non-selective and noncompetitive NMDAR antagonist; 25 mg/kg; SE + KET), CI-1041 (a GluN2B-containing NMDAR antagonist; 10 mg/kg; SE + CI group) or CP-101,606 (a NMDAR antagonist with great selectivity for NMDAR composed by GluN1/GluN2B diheteromers; 10 mg/kg; SE + CP group). Seven days after SE, brains were removed for Fluoro-Jade C staining and Iba1/ED1 immunolabeling. GluN2B-containing NMDAR blockade by CI-1041 or CP-101,606 did not terminate LiCl-pilocarpine-induced seizures. SE + SAL group presented intense neurodegeneration and Iba1+/ED1+ double-labeling in hippocampus (CA1 and dentate gyrus; DG) and amygdala (MePV nucleus). Administration of CP-101,606 did not alter this pattern. However, GluN2B-containing NMDAR blockade by CI-1041 reduced neurodegeneration and Iba1+/ED1+ double-labeling in hippocampus and amygdala similar to the reduction observed for SE + KET group. Our results indicate that GluN2B-containing NMDAR are involved in SE-induced neurodegeneration and microglial recruitment and activation, and suggest that stopping epileptic activity is not a condition required to prevent short-term brain damage in young animals.