Background Childhood acute lymphoblastic leukemia (cALL) involves the aberrant expression of lncRNAs. This study aimed to clarify the mechanisms of Lnc-TIM3 in cALL. Procedure The expression of Lnc-TIM3 in cALL bone marrow, cell lines were analyzed by quantitative real-time PCR (qRT-PCR). Cell migration, invasion were evaluated by transwell. CCK8 assays, soft agar colony formation, flowcytometry was used to measure the proliferation ability. The xenografts of zebrafish were analyzed to explore the roles of Lnc-TIM3 in vivo. The ceRNA regulatory mechanism of Lnc-TIM3 was evaluated by dual luciferase reporter assay. The protein levels of TIM3 were measured by western blot assay. Results Lnc-TIM3 was up-regulated in both cALL born marrow and cell lines. Lnc-TIM3 knockdown down-regulated TIM3 expression in cALL cells and remarkably restrained cALL progression both in vitro and in vivo. The phenotypic characteristics induced by Lnc-TIM3 knockdown were significantly reversed by miR-5094 inhibitor, and the downstream pathway was the TIM3/GAL9 autocrine stimulatory loop. Conclusion Lnc-TIM3 can sponge miR-5094 to up-regulate the expression of TIM3, thus promoting the development of cALL.