Schäffer's father, a carpenter, died at the age of 40, leaving his family in great poverty. Anna dropped out of school and worked as a maid from the age of fourteen, hoping eventually to be able to enter a religious order. But with family obligations she could barely make ends meet. In 1898, she had a vision of Christ that she was destined to endure long and painful suffering.

On February 4, 1901, while working at a laundry, Schäffer slipped and fell while reattaching a stovepipe and boiled her legs in the washing machine. She was taken to hospital, but nothing could be done about the painful burns. More than thirty surgical operations followed, and the wounds had to be carefully dressed, which also caused much pain. Despite the constant care of her Doctor, Dr. Waldin, skin grafts did not succeed and Schäffer became completely immobile. She was therefore forced to abandon her longtime dream of entering a religious order. Her mother was to care for her until the end of her life.

From 1910 mystical phenomena developed around her, including what could be described as stigmata, which she did her best to conceal from the public, and occasional waking visions which made her ecstatic. These developments brought no change in her attitude, though: she remained selfless, and promised prayers and letters for anyone who wanted them.

In 1925, she contracted colon cancer, and her paralysis spread to her spine, making it difficult to speak or write. On the morning of October 5, she received her final Holy Communion, and suddenly spoke: "Jesus, I live for you!" She died minutes later. At her funeral many already believed that they had known a saint.

After her death it became Common to visit her grave to have prayers answered. Since 1929, more than 15,000 miracles attributed to such prayers have been reported. In 1998, 551 miracles allegedly obtained through her intercession were recorded in the parish of Mindelstetten.

Schäffer was proposed for beatification in 1973. Over 20,000 letters and testimonies were collected as part of a detailed examination of her case.

During her beatification, 7 March 1999, Pope John Paul II said: "If we look to Blessed Anna Schäffer, we read in her life a living commentary on what Saint Paul wrote to the Romans: 'Hope does not disappoint, because the love of God has been poured out into our hearts through the Holy Spirit that has been given to us' (Rom. 5:5). She most certainly was not spared the struggle to abandon herself to the will of God. But she was given to grow in the correct understanding that weakness and suffering are the pages on which God writes His Gospel ... Her sickbed became the cradle of an apostolate that extended to the whole world."

In 2012, her notebook, entitled Thoughts and memories of my life of illness and my longing for the eternal homeland, was translated into English. On October 21, she was canonized by Pope Benedict XVI.