Genetic variants in ZMYND8, a chromatin regulator, are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder. While ZMYND8 has established roles in DNA damage response, oncogenesis and metastasis, its function in the brain remains poorly understood. Here, we generated hiPSC lines with ZMYND8 knockout and differentiated them into brain organoids to investigate the role of ZMYND8 in human brain development. Extensive characterisation of both hiPSC and brain organoids revealed widespread transcriptional and chromatin changes upon ZMYND8 knockout. We then integrated ATAC-seq and ChIP-seq to determine the direct targets of ZMYND8 regulation, and found ZMYND8 binds mainly to intronic and intergenic regions of the genome. Further, brain organoids generated from ZMYND8 knockout hiPSC had disrupted dorsoventral patterning, consistent with the upregulation of several SHH pathway genes in both hiPSC and brain organoids. Together, these findings support a role for ZMYND8 in regulating SHH pathway activity and dorsoventral patterning during human brain development, providing insight into how ZMYND8 dysfunction may contribute to neurodevelopmental disorders.