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Born in 1902, Pärsimägi was the son of a wealthy "gentleman farmer". In 1919, he participated in the Estonian War of Independence and was awarded a medal. After that, against his father's wishes, he went to Tartu to enrol at the new Pallas Art School, known for promoting modern art. In addition to the newer styles, such as Fauvism, he found himself influenced by Estonian folk art and by Konrad Mägi, who was a teacher there. He also studied with Ado Vabbe and Nikolai Triik and went on a study trip to Germany in 1923. That same year, he held his first exhibition. He interrupted his training several times to visit the family farm and paint landscapes.
He moved to Paris in 1937 with the financial support of his father, who had finally become reconciled to his son's career choice. While there, he studied at the Académie Colarossi and came under the influence of Paul Cézanne, although he became known as the "Estonian Matisse". At the outbreak of World War II, unlike most other Baltic artists, he refused to return to his homeland, which was now occupied by the Russians.
In 1941, he was arrested by the Gestapo and taken to Auschwitz via Drancy internment camp. The reasons for his arrest remain unclear. He was not Jewish, but may have been trying to help a Jewish friend or active in the French Resistance. Sexual orientation has also been cited as a possible motive. He was put to death the following year.
Because of his support for Estonian independence, his works were denied official recognition by the Soviet Union, but interest was renewed after 1991. The 100th anniversary of his birth was celebrated with an exhibition and many of his works are now at the Tartu Art Museum.