Pertusaria aptrootii is a species of crustose lichen in the family Pertusariaceae. It was described as a new species in 1998 by Alan W. Archer and John Alan Elix. The lichen occurs in Papua New Guinea, and is known from only two specimens collected at the type locality. The type was collected in Varirata National Park at an altitude of 800 m (2,600 ft), where it was found growing on conglomerate rock. It is named after Dutch lichenologist André Aptroot, who collected the type.