Rune \r(u)-ne\ as a boy's name is of Old Norse origin, and the meaning of Rune is "secret". Runes were the alphabet used by ancient German peoples from the third to the 13th century. They have an aura of mystery as they were translated only recently. Not related to the similar-sounding Roone.
Baby names that sound like Rune are Rane and Rene. Other similar baby names are June, Rube and Tune.