Abstract Aberrant activation of the sonic hedgehog (SHH) pathway is one of the key drivers of tumorigenesis in aggressive pediatric brain tumors. However, SHH pathway inhibitors for the treatment of brain tumors demonstrated only limited responses in clinical trials indicating that a better understanding of the human SHH pathway is needed. Using an integrative transcriptomic analysis of several thousand normal and neoplastic tissues with and without SHH activation, we identified HHIP-AS1 as an important long non-coding RNA that is strongly associated with SHH signaling in pediatric brain tumors. HHIP-AS1 expression was significantly up- and downregulated upon SHH activation or inhibition, respectively. We also revealed that HHIP-AS1 shares a bidirectional promoter with HHIP and that common transcription factors control both expressions. Transient and stable HHIP-AS1 knockdown (KD) led to a significant less aggressive phenotype of medulloblastoma and ATRT in vitro and in vivo (in cell lines, patient-derived primary cultures and in orthotopic mouse models). In detail, we observed a significant reduction of proliferation, cell viability, clonogenicity, and an induction of cell cycle arrest with a mitotic arrest upon HHIP-AS1 KD. Additionally, RNA sequencing and proteomic analysis unraveled cytoplasmic dynein complex 1 intermediate chain 2 (DYNC1I2), which is a key mitosis regulator, as a target of HHIP-AS1. Further investigations revealed that HHIP-AS1 stabilizes DYNC1I2 via RNA–RNA interaction and that DYNC1I2 overexpression rescued the observed phenotypes. Taken together, our analysis demonstrates that HHIP-AS1 promotes tumorigenesis in SHH-driven brain tumors and identify a novel lncRNA as a component in the human SHH signaling pathway. STEM CELLS