Treatment of pyoderma gangrenosum (PG) remains a challenge, and there are currently no specific or uniformly effective therapies. Although widespread or rapidly progressive disease often requires systemic treatment, localised and mild lesions may be effectively controlled with topical agents. The most frequently applied topical drugs are corticosteroids and calcineurin inhibitors. Recently, a patient with idiopathic PG of the lower limb was successfully treated with topical timolol and collagenase. Here, we report a case of a patient with collagenous colitis, ankylosing spondylitis and periumbilical PG. Persistent ulcerated skin lesions were successfully treated with topical timolol, although a flare of the underlying bowel disease temporarily interrupted the improvement. The case presented enhances the previously reported therapeutic potential of topical timolol in the treatment of PG. Control of chronic underlying disorders is critical to prevent rebound flares and maintain the benefit.