The Ecstasy of Rita Joe is about the plight of indigenous women in North America, particularly Canada. The larger or more general theme is the struggle that impoverished Native Americans and First Nations members experience in the predominantly white colonizer's society. However, the play also highlights the abuse indigenous women face from male members of their families and reservations.

The title of the play is a reference to the idea of Catholic saints displaying stigmata—the miraculous suffering of wounds that resemble those of Christ. Rita Joe experiences her own kind of "ecstasy" or stigmata in the form of injustice, oppression by patriarchy, and eventually rape and violent death. The playwright intends to convey that through her suffering, Rita transcends the pain and sorrow of mortals to become a saintly figure and a martyr essentially crucified by racist male violence.

Another theme concerns the flaws in the Canadian judicial system. The Canadian court has limited understanding of aboriginal cultures and their history of struggle in a modern Anglo-centric society. Rita not only has to fight for survival against dangerous men in the city and abusive, alcoholic men in her own reservation, but against the white male-dominant judicial system of Canada as well.

Throughout the play, the audience or reader can see the clash of white Canadian culture and indigenous culture. The priest represents one of the most effective weapons of colonialism: Christianity. When the priest and Rita get into an argument, she criticizes the Christian idea of God.

Lastly, the theme of the past haunting the protagonist is evident from the first act of the play. The past literally and figuratively "haunt" Rita by appearing in her dreams or appearing in the actual trial. Her past is laid bare before the court to examine.

The magistrate himself experiences a flashback in which the memory of a woman he once met in Cariboo country haunts him. It almost inspires him to be more lenient toward Rita, but he quickly regains his authoritarian mindset. This symbolizes the loss of humanity in a society engineered by corrupt political and economic systems.