The children, all aged between 10 and 15, were playing in the barn of a dairy farm in Nienburg, Lower Saxony, on Sunday, when the blaze broke out.
One boy was badly burned and is being treated in hospital. Four others managed to get out unharmed.
Officers worked at the scene all day on Monday, hunting through the wreckage of the eight-metre-high building which was burned to the ground in the fire.
Officials initially thought the missing girl might have panicked and run away. Helicopters had searched the area through Sunday night and a search party was assembled, but they could not find her.
Her body was found late on Monday among the ashes of the barn.