Purpose: A patient with heterozygous granular corneal dystrophy type 2 (GCD2) underwent phacoemulsification with multifocal intraocular lens insertion, and complained of visual discomfort. We investigated the cause of the discomfort and visual function in this case.Case summary: A 59-year-old woman with granular opacity had slit lamp photographs taken 5 years earlier. Two years later, she underwent phacoemulsification with multifocal intraocular lens (Trifocal AT Lisa tri toric 839MP<sup>®</sup>, Carl Zeiss Meditec AG, Inc., Jena, Germany) insertion in both eyes at a local clinic. She felt very uncomfortable after the surgery, but the granular and lattice opacities due to GCD2 of her corneas remained stationary for 5 years. Her visual acuity decreased from preoperatively (preoperative: right 0.5, left 0.6; last visit: right 0.3, left 0.4). Her contrast sensitivity was also decreased and the total higher order aberration was increased (right 1.590 μm, left 1.194 μm), compared to normal range.Conclusions: Multifocal intraocular lens insertion in cataract surgery can lead to severe declines in contrast sensitivity and visual acuity and increased higher-order aberration in a GCD2 patient. It may not be advisable to use multifocal intraocular lenses in a GCD2 patient.