Treatment options for Batten disease are extremely limited with research into new therapeutics urgently needed. Drug repurposing, where new uses are found for already existing drugs, is a potentially promising approach as it circumvents time consuming and expensive drug development. We investigated the ability to test the effects of repurposed drug candidates on Batten disease-specific induced pluripotent stem cell (iPSC)-derived models to discover potential new therapeutic compounds. Brain cells (neurons and astrocytes) were differentiated from iPSCs obtained from an individual with CLN3 type Batten disease, along with isogenic (CLN3-corrected) and healthy control iPSCs. Differentiation was confirmed via cell-specific marker expression. The phenotype of CLN3 and CLN3-corrected neurons and astrocytes was then compared to identify potential disease effects in CLN3 cells. Interestingly, CLN3 neurons demonstrated altered lysosomal enzyme expression whilst CLN3 astrocytes demonstrated abnormal cytokine secretion compared CLN3-corrected cells, demonstrating a disease phenotype. Following this, the effects of 4 candidate drugs identified via a computational drug repurposing analysis were tested on CLN3 neurons and astrocytes. The tested compounds had minimal effects on cell viability, however, some of the compounds were able to increase lysosomal enzyme expression in CLN3 neurons and reduce cytokine secretion CLN3 astrocytes. Furthermore, some of the drugs were found to modulate lipofuscin content in CLN3 cells. These results demonstrate that computational drug repurposing analysis when combined with disease-specific iPSC models is a potentially powerful approach to identify new therapeutics for rare but devastating disorders like Batten disease.