From 1910 to 1962 the city was known as Hollandia and was the capital of a district of the same name in the northeast of West New Guinea. The city was renamed as Kota Baru for the United Nations ceremony of 1st May 1963.
The northern part of Dutch New Guinea was occupied by Japanese forces in 1942. Allied forces drove out the Japanese after amphibious landings near Hollandia, from April 21, 1944. The area served as General Douglas MacArthur's headquarters until the conquest of the Philippines in March 1945. Over twenty U.S. bases were established and half a million US personnel moved through the area.
In 1945, the Dutch made Hollandia the capital of Netherlands New Guinea. After the territory was handed over to the United Nations, on October 1, 1962, the city became known by the Indonesian name Kota Baru, and retained the name when Indonesia took control, on May 1, 1963. The city was briefly renamed Sukarnopura, after President Sukarno, until the end of 1968, when it acquired its present name. The literal meaning of Jayapura, as of Jaipur in Rajasthan, is 'City of Victory' (Sanskrit jaya: "military victory"; pura: "city").