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Introduction Study of TOfacitinib for the treatment of chronic PouchITis (STOPit) is a national, investigator-led, multicentre, open-label induction with randomised, double-blind, placebo-controlled maintenance trial to determine the effectiveness of tofacitinib to induce and maintain clinical remission in chronic pouchitis patients. The primary objective of STOPit is to evaluate the clinical response to tofacitinib, compared with placebo, using the validated modified Pouchitis Disease Activity Index score. Secondary objectives include clinical response and remission rates, endoscopic response and mucosal healing rates in induction and maintenance phases; rates of flare and recapturing response in open label extension phase; the effect of tofacitinib on clinical biomarkers and quality of life; and safety of tofacitinib use for treatment of chronic pouchitis. Study period is up to ten months, with five visits and three pouchoscopies.Methods and analysis Adults with ulcerative colitis who have undergone total proctocolectomy and ileal pouch-anal anastomosis and have chronic pouchitis are eligible. Participants receive open-label 10 mg two times per day tofacitinib for 8 weeks. Clinical responders at the end of week 8 will be randomised to either tofacitinib or placebo in the maintenance phase. Non-responders will receive extended induction dosing for a further 8 weeks. Persistent non-responders exit the study and responders will proceed to maintenance randomisation. Randomised individuals will be followed for 24 weeks. Patients experiencing a flare of symptoms during the maintenance phase will be eligible to receive open-label tofacitinib. Efficacy and safety data will be evaluated at 12 weeks after termination from the study. Target sample size is 72 patients to be randomised into maintenance to achieve sufficient power. Data analysis is planned to commence in October 2026.Ethics and dissemination Ethics approval was granted (Project ID 66809) and the trial was notified (CTN: CT-2020-CTN-04866-1; ANZCTR: 381128) prior to commencement. The study will be conducted in accordance with National Health and Medical Research Council (NHMRC) guidelines, and findings will be published in a peer-reviewed journal.Trial registration number CTN: CT-2020-CTN-04866-1.