Non-penetrating trabeculectomy (NPT) is effective in preventing numerous postoperative complications encountered with trabeculectomy. Recently, NPT has been modified to further reduce intraocular pressure (IOP) by combining other techniques. However, these modified NPT methods would make the globe even weaker than NPT alone. Here, we report a case of iris prolapse caused by blunt ocular trauma after NPT with sinusotomy and mitomycin C treatment. A 68-year-old man, who underwent NPT with sinusotomy and mitomycin C treatment, suffered from blunt ocular trauma to his left eye 28 days after surgery. The iris prolapsed from the sinusotomy site. Iridectomy, scleral suturing, and pars plana vitrectomy were performed. The bleb was absent post-re-operatively. Iris prolapse occurs uncommonly following simple NPT. However, additional sinusotomy and mitomycin C treatment render the globe weaker, and iris prolapse might occur. Iris prolapse increases risks in developing secondary infections and a loss of the filtration bleb. Thus, precautions are needed postoperatively.