Maria Antonina was born in Witkowice near Ostrava where her parents arrived in 1879 from Węgierska Górka in the Austrian Partition in search of sustenance; her father worked at a foundry. In 1885 the family returned to her mother's hometown in Węgierska Górka close to Żywiec, and settled in Bielsko nearby. In 1901 Maria Antonina entered the Congregation of School Sisters of Notre Dame, a worldwide Roman Catholic order devoted to providing primary, secondary, and post-secondary education. She passed her maturation exams in 1906, and became a professed sister. Ten years before the rebirth of sovereign Poland Kratochwil was sent to Karviná near Cieszyn to teach at a Polish elementary school, twice: between 1906–09, and 1910–17. Already in independent Poland she settled in Lwów in the Kresy region where she taught until 1925. She served as director of Catholic boarding school there in 1925–32; relocated to the town of Tłumacz to train other sisters as teachers, and returned to Lwów, where she was appointed director of a school for candidates in 1931–39.
Following the Soviet invasion of Polandat the beginning of World War II, the NKVD authorities closed down the Polish schools in Lwów and dismissed the sisters. Maria Antonina relocated with her nuns to Mikuliczyn in December 1939. The Soviets raided the convent in Mikuliczyn, nationalized it, and expelled the nuns; they were prohibited from wearing their religious habits ever again. Lwów was taken over by the Germans in June 1941 at the onset of Operation Barbarossa. A year later, Sister Kratochwil was arrested by the Gestapo on 9 July 1942, along with six other nuns, and thrown into prison in Stanisławów, a provincial capital with a large Polish Jewish population entrapped in the Stanisławów Ghetto. The nuns were kept in a cell with dozens of other women. Sister Kratochwil intervened against the brutal treatment of Jewish female prisoners by the Gestapo office run by the notorious Holocaust perpetratorSS-Hauptsturmführer Hans Krueger. As punishment for her audacity, Kratochwil was subjected to a torturous beating. Returned to the cell all bloodied, she could no longer lie on her back. The six sisters were released at the end of September 1942, after weeks of interrogations. Maria Antonina died from her injuries on 2 October 1942 in a hospital, five days after her release from prison. She was buried in Sapieżyński Cemetery in Stanisławów. Sister Kratochwil was declared patron of Shalom at the 3rd International Shalom meeting held in El Salvador in August 2000. A short book was published about her life in 2001.