Kasumigaseki Country Club's executive board is said to have decided on the change after discussions with members.
The bar on women being full members came under scrutiny when Tokyo governor Yuriko Koike urged a change. Other critics said the ban was against the Olympic spirit.
Yoshiro Mori, president of the Tokyo Olympic organizing committee, said he was grateful to members for their "understanding and cooperation."
Set up in 1929, Kasumigaseki is one of Japan's most prestigious golf clubs.