“Perinatal programming” is a phenomenon describing how early life environmental conditions can produce long-term physiological alterations that either enhance or inhibit adaptive functioning. Previously, we have demonstrated that neonatal exposure to lipopolysaccharide (LPS) predisposes to anxiety-like behaviour in later life, which was associated with changes to the neuroendocrine response to stress. Given the known interactions between the neuroendocrine and neuroimmune systems, here we investigated whether neonatal exposure to a bacterial mimetic alters neuroimmune responses to acute stress in adulthood. Male and female Wistar rats were administered LPS (0.05 mg/kg, i.p.), or saline vehicle (equivolume) on days 3 and 5 post-partum. One group of rats was euthanised following early life treatment to assess immediate hypothalamic–pituitary–adrenal axis and central cytokine responses to treatment. A second group was assessed in adulthood (85 days) following exposure to either a “stress” (30-min restraint) or “no stress” condition. Blood was collected from all rats at baseline, 30, 60 and 90 min after “stress”, “no stress” treatment to assess peripheral corticosterone responses, and brains were collected 180 min following baseline to assess hippocampal content of interleukin-1β (IL-1β), tumour necrosis factor-α (TNFα) and IL-6 protein. Radioimmunoassay revealed that neonatal LPS treatment resulted in a prolonged corticosterone response to stress in adulthood compared to controls (p < 0.05). Enzyme-linked-immunosorbent assays revealed no group differences in hippocampal IL-6 content. However, brain IL-1β and TNFα protein concentrations were significantly greater in rats neonatally exposed to LPS and then exposed to stress in adulthood when compared to all other groups (p < 0.05). These findings suggest that early life bacterial toxin exposure results in a prolonged neuroendocrine response to acute stress in adulthood, which may be a consequence of increased release of IL-1β and TNFα in the brain.