Operation Liberate Men (2003)

Blurb:
Ashamed of failing her high school entrance exam, a 16-year-old tomboy Sooha just wants to disappear off the face of the Earth. However, when she yells it out loud a mysterious stranger named Ganesha approaches with an offer. He comes from a magical realm called the Para Kingdom ruled by a female military hierarchy that enslaves the male population. Ganesha offers to grant Sooha’s wish if she will help liberate the men. Thinking his country sounds like paradise, she instantly agrees. But, when she arrives the men look to her as their new leader and Sooha learns that fate has a funny way of leading people to their destiny.

Source: www.anisearch.com/manga/6172