"What a strange surname!" the 82-year-old ailing former Cuban dictator wrote in his column in the Communist Party newspaper Gramma.
"It appears Spanish, easy to pronounce, but it's not," Castro wrote. "Never in my life have I heard or read about any student or compatriot with that name, among tens of thousands."
Emanuel -- sometimes spelled Emmanuel or Immanuel -- is Hebrew for "God is with us."
It is a common Christian and Jewish name that first appears in the biblical Book of Isaiah. It is featured in the popular Advent and Christmas hymn "O come, O come, Emanuel."
The name in Spanish is Manuel, usually used as a first name.
Castro wondered in his column if Rahm Emanuel's name derived from 18th century German philosopher Immanuel Kant, "who together with Aristotle and Plato formed a trio of philosophers that have most influenced human thinking."
His column also spoke about the U.S. economic-stimulus package, which Castro said would not work.
"Obama, Emanuel and all of the brilliant politicians and economists who have come together would not suffice to solve the growing problems of U.S. capitalist society," he wrote.