The lack of advancement in the treatment of glioblastoma (GBM) over the past two decades calls for more innovation to address the inter- and intra-patient heterogeneity confounding modern target-directed drug discovery strategies. In this study, we incorporate a panel of patient-derived GBM stem cell lines into an automated and unbiased “cell painting” assay to quantify multiple GBM stem cell phenotypes. By screening several compound libraries, followed by dose-response validation of hit compounds, we present a comprehensive survey of distinct pharmacological classes and druggable targets upon multiple GBM stem cell phenotypes. We further characterize two validated target classes, histone deacetylase and cyclin dependent kinase inhibitors. We demonstrate that unbiased Cell Painting phenotypic screening is a productive approach to identifying new targets, drug classes and future drug combinations that address the heterogeneity of GBM. We provide all GBM cell painting data for each compound perturbation for the research community to explore further.