This study aimed to investigate the change of disease distribution in pediatric neurology inpatients during the COVID-19 outbreak in southwest China. We retrospectively extracted the demographic data and diagnosis of discharged patients registered at pediatric neurology department of Chengdu Women’s and Children’s Central Hospital from January 1 to July 31, 2019 and January 1 to July 31, 2020. Total number of inpatients decreased during COVID-19 outbreak. Children diagnosed as febrile seizure caused by infection (1799/60.7% vs 980/59%, P = 0.141), dyskinesia (31/1.0% vs 28/1.7%, P = 0.075) and benign intracranial hypertension (41/1.4% vs 21/1.3%, P = 0.791) did not change. While children diagnosed as epilepsy (304/10.3% vs 348/21%, P < 0.001), migraine (25/0.8% vs 31/1.9%, P = 0.003), mental disease (24/0.8% vs 43/2.6%, P < 0.001) and peripheral neuropathy (38/1.3% vs 43/2.6%, P = 0.001) increased in 2020. Children diagnosed as intracranial infection (535/18% vs113/6.8%, P < 0.001) and myopathy (106/3.6% in vs 22/2.0%, P = 0.003) reduced in 2020. Conclusions: We found a significant increase in the proportion of mood-related diseases, while disease caused by infection decreased. We should pay attention to children’s mental state during the public health epidemic and the management of chronic disease.