Patients with atopic dermatitis undergoing penetrating keratoplasty (PKP) face a high risk of postoperative complications. Endothelial keratoplasty may be a safer alternative for such patients, including those with abnormal anterior chamber anatomy. 3 male patients, aged 33 to 44, presented with blurred vision at Keio University Hospital. Bullous keratopathy was diagnosed through slit-lamp examination and specular microscopy. Two patients had well-controlled systemic atopic dermatitis, while 1 had blepharitis associated with atopic dermatitis. Two patients had peripheral anterior synechia, and 2 had undergone glaucoma surgery before keratoplasty. Non-Descemet stripping endothelial keratoplasty (nDSAEK) was performed by a single surgeon. The best-corrected visual acuity ranged from 0.7 to 1.5 logMAR before surgery and from 0.2 to 2.3 logMAR after surgery. One year post-surgery, the graft remained clear in 2 cases; however, in the case of repeated glaucoma surgeries after nDSAEK, the graft became edematous. Corneal endothelial cell density was 1586 and 1988 cells/mm² in 2 cases and undetectable in the failed case. The follow-up period ranged from 2.5 to 9 years. Despite the presence of peripheral anterior synechia or prior glaucoma surgery, some patients experienced a favorable long-term postoperative course following nDSAEK. This procedure may offer a safer alternative for treating patients with atopic dermatitis who have ocular complications that present a high risk for PKP.