A 4-year-old boy developed unilateral, total limbal stem cell deficiency (LSCD) following an acid injury. A stable ocular surface was achieved with autologous simple limbal epithelial transplantation (SLET), performed 4 months after the injury. Focal areas of conjunctivalisation were noted in the postoperative period. These were addressed using a novel modification of SLET. A very small piece of limbus from the healthy eye was split into multiple pieces, and applied to the bare corneal stroma with fibrin glue after pannus resection. The surface was covered with amniotic membrane. This resulted in a stable surface, and visual acuity improved to 20/50. The donor remained healthy despite two biopsies being harvested. This case demonstrates that early ocular surface reconstruction may be considered in children with LSCD if amblyopia is a concern. Customised SLET allows surgeons to tackle focal recurrences of LSCD effectively, using minimal limbal tissue from the donor site.