Objective: To explore the immune characteristics and short-term prognosis of children with autoimmune encephalitis (AE), then to analyse the relationship between them. Methods: A total of 78 children with AE were identified through the clinic database and inpatient consults in Tianjin Children’s Hospital (238 Long-Yan Road, Bei-Chen District, Tianjin, China) from January 2018 to January 2021. Based on the recent follow-up (one-year follow-up) of the modified Rankin Scale (mRS) prognosis score, they were divided into a good prognosis group (59 cases, mRS <3 points) and a poor prognosis group (19 cases, mRS ≥3 points). The immune function characteristics of the two groups of children with AE were compared using Spearman correlation to analyse the mRS score and immune function indicators (IgA, IgG, IgM, CD4, CD8, CD4/CD8), and using binary logistic regression to analyse the factors affecting the prognosis of children with AE. Results: The differences in age, consciousness disorder, limb dyskinesia, cognitive impairment, onset type, mRS score at admission, and immune function status during remission between the two groups were statistically significant (p < 0.05). The mRS score of the good prognosis group at admission was significantly lower than that of the poor prognosis group (2.65 ± 0.76 vs 3.05 ± 0.71, p < 0.05). IgA (0.61 ± 0.19 vs 0.87 ± 0.25, p < 0.001), IgG (8.17 ± 1.12 vs 9.02 ± 1.39, p = 0.001). IgM (1.01 ± 0.26 vs 1.23 ± 0.33, p < 0.001) in the good prognosis group were significantly lower than those in the poor prognosis group, while CD4 (36.35 ± 8.74 vs 23.89 ± 6.97, p < 0.001) and CD4/CD8 (1.68 ± 0.32 vs 1.01 ± 0.24, p = 0.001) were significantly higher than those in the poor prognosis group. Spearman correlation analysis showed that the mRS score at admission was significantly negatively correlated with CD4/CD8 (r =−0.775, p < 0.001), but not significantly correlated with other immune function indexes. Binary logistic regression showed that age (OR = 0.385; 95% CI = 0.200–0.741), consciousness disorder (OR = 39.3569; 95% CI = 4.073–380.262), limb movement disorder (OR = 17.107; 95% CI = 2.769–105.701), and abnormal immune function in remission (OR = 0.050; 95% CI = 0.007–0.372) were risk factors for poor prognosis in children with AE. Conclusion: There is a close correlation between mRS and immune function index CD4/CD8 in children with AE when they are admitted to the hospital. Young age, disturbance of consciousness, limb dyskinesia, and abnormal immune function in remission are risk factors for poor prognosis of children with AE. More attention should be paid in clinical treatment.