Malignant glaucoma is characterized by ciliary block or aqueous misdirection, shallowing of the anterior chamber with elevated intraocular pressure (IOP), resistance to treatment, and rapid progression to blindness. However, the exact pathogenic mechanism is yet to be established. Here, we report a case of malignant glaucoma caused by immediate primary phacoemulsification for acute primary angle closure (APAC). A 90-year-old woman, who had experienced right eye pain and blurred vision one day prior, had a cataract in the same eye without phacodonesis. The right eye IOP was 39 mmHg, preoperative anterior chamber depth was 1.00 mm, and the axial length was 22.31 mm. We diagnosed APAC in the right eye and performed phacoemulsification. On postoperative day one, the IOP decreased to the normal range (15 mmHg), the anterior chamber deepened, and the angle became open. However, one week after phacoemulsification, the anterior chamber and angle became shallower and closer again. We diagnosed the patient with malignant glaucoma, performed hyaloid-zonulo-iridectomy, and administered 1% atropine eye drops postoperatively. As a result, the IOP was limited to a 10 mmHg range with an open angle and deep anterior chamber. Malignant glaucoma can be caused by immediate primary phacoemulsification for APAC.