Summary Nociceptive response belongs to a basic animal behavior facilitating adaptability and survival upon external or internal stimuli. Fish, similarly to higher vertebrates, also possess nociceptive machinery. Current protocols involving procedures performed on adult zebrafish including heart cryoinjury do not, however, take into account the adverse effects including pain that may potentially arise from these methodologies. Here, we assess the effect of two analgesics, lidocaine and morphine, followed after heart cryoinjury in zebrafish. Monitoring swimming behavior together with histology and gene expression analysis at the single cell level using scRNA sequencing and RNAscope fluorescent in situ hybridization technology, we show morphine, but not lidocaine, significantly improves animal welfare 6 hours post-cryoinjury, without impairing the heart regeneration process. Altogether, we propose morphine to be considered as the analgesic of choice to reduce post-surgical pain in adult zebrafish. Highlights Cryoinury could be considered as a potential noxious stimulus in adult zebrafish. Morphine but not lidocaine treatment effectively alleviates noxious effects post-cryoinjury. Lidocaine treatment delays heart repair and regeneration. 6 hours Morphine treatment after cryoinjury does not impede heart regeneration.