The adhesion G-protein-coupled receptor is a seven-transmembrane receptor protein with a complex structure. ImpairedGPR56has been found to cause developmental damage to the human brain, resulting in intellectual disability and motor dysfunction. To date, studies ongpr56deficiency in zebrafish have been limited to the nervous system, and there have been no reports of its systemic effects on juvenile fish at developmental stages. In order to explore the function ofgpr56in zebrafish, the CRISPR/Cas9 gene-editing system was used to construct agpr56-knockout zebrafish. Subsequently, the differentially expressed genes (DEGs) at the transcriptional level between the 3 days post fertilization (dpf) homozygotes of thegpr56mutation and the wildtype zebrafish were analyzed via RNA-seq. The results of the clustering analysis, quantitative PCR (qPCR), and in situ hybridization demonstrated that the expression of innate immunity-related genes in the mutant was disordered, and multiple genes encoding digestive enzymes of the pancreatic exocrine glands were significantly downregulated in the mutant. Motor ability tests demonstrated that thegpr56−/−zebrafish were more active, and this change was more pronounced in the presence of cold and additional stimuli. In conclusion, our results revealed the effect ofgpr56deletion on the gene expression of juvenile zebrafish and found that thegpr56mutant was extremely active, providing an important clue for studying the mechanism ofgpr56in the development of juvenile zebrafish.