A 7-year-old female presented with blepharophimosis ptosis epicanthus inversus syndrome with congenital hypothyroidism and brachydactyly. She displayed typical manifestations of type II blepharophimosis ptosis epicanthus inversus syndrome (normal uterus position, ovarian volume, and normal serum hormone levels). She takes levothyroxine sodium daily due to her congenital hypothyroidism. Karyotype analysis and genetic analysis of FOXL2 coding sequence was found to be normal. mtDNA A3243G, A8344G, 8993, and 13513 genes were also normal. The absence of mutations excluded mitochondrial encephalomyopathies. To the best of our knowledge, this is the first reported case of blepharophimosis ptosis epicanthus inversus syndrome with congenital hypothyroidism and brachydactyly.