Shortly before Anne Frank went into hiding from the Nazis, she gave some of her belongings to a non-Jewish friend who lived next door.
The neighbour, Toosje Kupers who is now 83, kept the marbles along with a tea set and a book. It was only when she was moving last year that she thought about telling the museum.
Kupers told a Dutch television news station that she didn't consider the marbles that special. She said that shortly before the Frank family went into hiding, Anne approached her and asked for a favour.
"I'm worried about my marbles. I'm scared they might fall into the wrong hands. Could you keep them for me for a little while?"
The Frank family went into hiding in 1942 in a concealed apartment above a warehouse. Everyone but a few select friends thought they had gone to stay with family in Switzerland.
Both of them could not have guessed that Anne, who died in Bergen-Belsen concentration camp, would never return. Toosje's family also took in the Frank's cat, Moortje. Anne's diary was found and published after the war by her father, Otto, who was the only member of the family to survive.
Museum head of collections, Teresian de Silva, said:
"So many people know Anne because of the diary, but the marbles are a reminder she was just a little girl."
The Anne Frank House Museum said that the toys will go on display at the Kunsthal Gallery in Rotterdam.