Background <p>Niemann-Pick disease type C1 (NPC1) is caused by <i>NPC1</i> gene mutations, resulting in Purkinje cell degeneration and death, glial cell activation, and progressive neurodegeneration. Menstrual blood-derived endometrial stem cells (MenSCs) have been explored as a promising tool for treating neurodegenerative diseases due to their wide range of sources, non-invasive nature, and regular collection methods.</p> Objectives <p>This study aims to investigate whether MenSCs can improve neuroinflammation and apoptosis in NPC1 mutant cell (<i>Npc1</i>^KO BV2 cell line) and mice (<i>Npc1</i>^{<i>−/−</i>} mice), and explore their underlying mechanisms.</p> Methods <p>MenSCs were transplanted into the 4-week-old <i>Npc1</i>^{<i>−/−</i>} mice cerebellum through stereotaxic injection, and their effects on weight, behavior, and survival were assessed. The activation of glial cells and the survival of neurons were detected by immunofluorescence technology, and the expression level of related inflammatory factors and apoptotic proteins was detected by western blotting. The transcriptome changes in cerebellum after MenSCs transplantation were analyzed by transcriptome sequencing. The mechanism by which MenSCs treat NPC1 was validated at the cellular level using the activator butyzamide.</p> Results <p>MenSCs transplantation could slow down the rate of weight loss and improve motor coordination in <i>Npc1</i>^{<i>−/−</i>} mice, but had no significant improvement in lifespan. MenSCs could mitigate the activation of glial cells, alleviate neuroinflammation, reduce cell apoptosis, and increase the number of mature neurons and Purkinje cells in the cerebellum. Transcriptome analyses results indicated that the JAK/STAT signaling pathway changed across different groups. Compared with age-matched <i>Npc1</i>^<i>+/+</i> mice, the protein expression levels of P-JAK2 and P-STAT3, the ratios of P-JAK2/JAK2 and P-STAT3/STAT3 were increased in the cerebellum of 5-week-old <i>Npc1</i>^{<i>−/−</i>} mice in the PBS group; compared with age-matched <i>Npc1</i>^{<i>−/−</i>} mice in the PBS group, the protein expression levels of P-JAK2 and P-STAT3, the ratios of P-JAK2/JAK2 and P-STAT3/STAT3 were decreased after MenSCs transplantation. Finally, treating <i>Npc1</i>^<i>KO</i> BV2 cells with butyzamide further confirmed that MenSCs relieve inflammation and apoptosis caused by <i>Npc1</i> gene mutations through JAK2/STAT3 signaling pathway.</p> Conclusion <p>Our study demonstrate that MenSCs ameliorate neuroinflammation and apoptosis in NPC1 mutant cell and mice through JAK2/STAT3 signaling pathway.</p>