INTRODUCTION AND IMPORTANCE: Scleritis, an inflammation of the sclera, can result from infections, autoimmune diseases, or systemic conditions like connective tissue disorders. Secondary glaucoma from scleritis is rare but challenging to manage. This report presents a case of iStent migration in a patient with refractory idiopathic scleritis. CASE REPORT: A 56-year-old female with a history of diabetes mellitus, hypertension, and refractory scleritis, complicated by secondary glaucoma. Despite multiple interventions, including selective laser trabeculoplasty, deep sclerectomy, and phacoemulsification with toric intraocular lens (IOL) implantation. The patient required the insertion of an iStent in the left eye. Postoperatively, the iStent migrated into the subconjunctival space, leading to elevated intraocular pressure (IOP) and necessitating further management. Examination revealed severe scleral thinning and uveal prolapse, with significantly elevated IOP in the left eye. Medical management included systemic immunosuppressants and ocular hypotensive agents. DISCUSSION: This case suggests that severe scleral thinning and chronic inflammation compromised the anchoring of the iStent, resulting in migration and elevated IOP. This complication underscores the need for careful surgical planning in similar cases. CONCLUSION: This case underscores the complexities of managing secondary glaucoma in the context of refractory scleritis and highlights the critical need for meticulous surgical technique and rigorous postoperative follow-up to address potential complications such as iStent migration.