CEP290 gene mutations are linked to Joubert syndrome-related disorders (JSRD) which present with various symptoms, including brain malformation, retinal degeneration, and kidney disorders. It remains unclear how patients with JSRD having CEP290 gene mutations lead to kidney disorders, particularly polycystic kidney disease including nephronophthisis (NPH). To address this question, Xenopus CEP290 (xCEP290) was depleted using morpholino oligonucleotides against xCEP290 in Xenopus embryos. xCEP290 morphants exhibited edema and dilated pronephric tubule, indicative of renal dysfunction. Next, RNA-seq analysis was performed to explore which signals and molecules are important for the formation of dilated pronephric tubule observed in the xCEP290 morphant kidney. The hallmark gene set associated with the IL-6/JAK/STAT3 signaling pathway was upregulated in xCEP290 morphant kidney, and inhibition of this signaling by JAK inhibitor ruxolitinib suppressed the dilated pronephric tubule in xCEP290 morphants. Furthermore, the expression level of transcription factor Xenopus FOSL1 (xFOSL1), whose gene expression is regulated by IL-6 signaling, was upregulated in xCEP290 morphant kidney, and overexpression of xFOSL1 induced pronephric tubular dilation. These results together revealed that abnormal activation of IL-6/JAK/STAT3/FOSL1 signal axis is responsible for dilated pronephric tubule resembling cystic lesions observed in polycystic kidney disease of JSRD patients with CEP290 gene mutations.