Background: To present a case of conjunctival lymphangioma in a 4-year-old girl with tuberous sclerosis complex. Methods/results: A 4-year-old girl presented with a relapsing cystic lesion of the bulbar conjunctiva in the right eye with string-of-pearl-like dilation of lymphatic vessels and right-sided facial swelling with mild pain. Best-corrected vision was not impaired. Examination of the skin revealed three hypomelanotic macules and a lumbal Shagreen patch. Magnetic resonance imaging (MRI) findings displayed minimal enhancement of buccal fat on the right side. Cranial and orbital MRI showed signal enhancement in the right cortical and subcortical areas. Genetic analysis revealed a heterozygous deletion encompassing exon 1 and 2 of the TSC1 gene (tuberous sclerosis complex 1 gene), confirming the diagnosis of tuberous sclerosis complex. Conclusion: In conjunctival lymphangioma, tuberous sclerosis complex should be considered as the primary disease.