Treatment options for intracerebral haemorrhage (ICH) patients are limited. Understanding the neuroinflammatory processes resulting from bleeding in the brain is paramount to identifying an appropriate therapy. Zebrafish larvae represent a valuable, alternative in vivo system to study ICH pre clinically. The bubblehead mutant zebrafish larvae displays spontaneous ICH which develops quickly, and the peak inflammatory response is observed 24 hours after injury. In this study, we isolated neutrophil and macrophage populations from haemorrhaged larvae and carried out RNA-Seq analysis to identify differences in gene expression in comparison with non-haemorrhaged sibling controls. This is the first transcriptomic dataset generated from an experimental model of spontaneous ICH and will provide a useful resource for investigating the complex transcriptomic processes that regulate inflammation following haemorrhagic stroke.