Long non-coding RNAs (lncRNAs) have already been documented to become the therapeutic targets for neuropathic pain. Here, this work focused on exploring the specific mechanism underlying Kcnq1 overlapping transcript 1 (kcnq1ot1) in neuropathic pain. Sciatic nerve chronic constriction injury (CCI) in vivo and LPS-stimulated microglia BV2 cell injury in vitro were adopted to construct neuropathic pain models. Expressions of kcnq1ot1, MyD88, and microglia activation marker Iba-1 were measured. In this study, we carried out fluorescence in-situ Hybridization (FISH) and immunofluorescence for examining Kcnq1ot1 localization within microglial cells in mouse spinal dorsal horn. Subsequently, we evaluated binding between Kcnq1ot1 and Myd88, together with the expressions of IL-1β, IL-6, TNF-α, and Myd88 ubiquitination. Kcnq1ot1 levels decreased within CCI mice and LPS-induced BV2 cells. According to the results of FISH and immunofluorescence, Kcnq1ot1 is located in microglia. Overexpression of Kcnq1ot1 suppressed Iba-1, IL-1β, IL-6 together with TNF-α expression. RNA pull-down and RIP assay confirmed that Kcnq1ot1 bound to Myd88. In addition, Kcnq1ot1 overexpression promoted the degradation, enhanced the ubiquitination, and reduced protein level of Myd88. Overexpression of Myd88 eliminated the effects of Kcnq1ot1 overexpression on Iba-1level and production of pro-inflammatory cytokines. Further in vivo results revealed that increased Kcnq1ot1 level alleviated neuropathic pain and myelinated nerve fiber injury of CCI mice. Kcnq1ot1 downregulated Myd88 protein expression by binding to Myd88 and promoting its ubiquitination, which in turn suppressed microglia activation, pro-inflammatory cytokine production, and relieved neuropathic pain.