Seizures are due to excessive, synchronous neuronal firing in the brain and are characteristic of epilepsy, the fourth most prevalent neurological disease. We report handling‐induced and spontaneous seizures in mice deficient for CD39, a cell‐surface ATPase highly expressed on microglial cells. CD39^−/− mice with handling‐induced seizures had normal input–output curves and paired‐pulse ratio measured from hippocampal slices and lacked microgliosis, astrogliosis or overt cell loss in the hippocampus and cortex. As expected, however, the cerebrospinal fluid of CD39^−/− mice contained increased levels of ATP and decreased levels of adenosine. To determine if immune activation was involved in seizure progression, we challenged mice with lipopolysaccharide (LPS) and measured the effect on microglia activation and seizure severity. Systemic LPS challenge resulted in increased cortical staining of Iba1/CD68 and gene array data from purified microglia predicted increased expression of interleukin‐8, triggering receptor expressed on myeloid cells 1, p38, pattern recognition receptors, death receptor, nuclear factor‐κB , complement, acute phase, and interleukin‐6 signalling pathways in CD39^−/− versus CD39^+/+ mice. However, LPS treatment did not affect handling‐induced seizures. In addition, microglia‐specific CD39 deletion in adult mice was not sufficient to cause seizures, suggesting instead that altered expression of CD39 during development or on non‐microglial cells such as vascular endothelial cells may promote the seizure phenotype. In summary, we show a correlation between altered extracellular ATP/adenosine ratio and a previously unreported seizure phenotype in CD39^−/− mice. This work provides groundwork for further elucidation of the underlying mechanisms of epilepsy.