The stress resilience and cell survival factor FOXO3 has neuroprotective effects in several models of neurodegenerative diseases, including Huntington’s disease (HD). However, how this transcription factor may precisely promote neuroprotection against proteotoxic stress in neurodegenerative diseases such as HD remains unknown. Additionally, FOXO3 transcriptional and neuroprotective activity in HD may be altered by abnormal levels of FOXO3 co-factors that normally function into neurodevelopmental pathways. To evaluate alteration of FOXO3 gene regulation in HD, we used genome-wide analysis to identify FOXO3 direct targets in isogenic human neural stem cells expressing mutant huntingtin or the wild-type protein (An et al., Cell Stem Cell 2012). We also investigated how signalling by Ryk, an axon guidance receptor that functions in Wnt signalling and that modifies FOXO3 activity in HD cells (Tourette et al., PLoS Biol 2014), may effect FOXO3 gene regulation and target repertoire. The results emphasise FOXO3 target subsets that are altered by neurodevelopmental signalling or mutant huntingtin, or both, during cell differentiation. The biological implication and HD relevance of this model will be discussed.