Upon graduating from Hosei University, Onaga returned to Okinawa shortly before the United States returen the islands to Japan in 1972. After briefly working for a construction company, Onaga ran and was elected to the Naha City Council in 1985 for the Liberal Democratic Party. Onaga went on to become a member of the Okinawa Prefectural Assembly in 1992.
Mayoralty
Onaga became the Mayor of Naha in 2000, running as an independent candidate. During his term as mayor, Onaga supported a plan to relocate the Marine Corps Air Station Futenma, located in an urban area near Naha, to a more remote area of the island in Nago. According to his biographer, Onaga gave this support reluctantly. Onaga thought the base was against the will of the Okinawan people but he did not feel as mayor he has the power to oppose the Japanese central government, who supported the move. Onaga served four terms as mayor until he was elected as the Governor of Okinawa Prefecture in 2014.
Governorship
Onaga was elected to the governorship defeating the incumbent, Hirokazu Nakaima. His campaign was based on opposing the relocation of the Futenma Base within Okinawa, and ending U.S. military presence in Okinawa. In October 2015, Onaga revoked the land reclamation permit needed for continued work on the base. This stance also made him a target of regular smear campaign by some Japanese right-wing activists on the internet. For example, in April 2015, Toshio Tamogami, former chief of the Japanese Air Self-Defense Force tweeted that Onaga's daughter had studied in Beijing and married a Chinese Communist Party official, an allegation intended to link Onaga and his opposition to the American bases in Okinawa to the CCP.
Death
Onaga was diagnosed with a pancreatic tumor in April 2018, then had a surgery and returned to work in May. According to The New York Times, Onaga looked "visibly weakened" during a war-memorial service in June. Onaga died at a hospital in Urasoe on 8 August 2018, four days after announcing his "last resort" of withdrawing planning permission for the construction of the U.S. military. His deputy, Kiichiro Jahana, took over the governorship ad interim, and announced that Around 70,000 people rallied in Okinawa on 11 August 2018 in honour of Onaga's memory and his struggle against the relocation of U.S. Marine Corps Air Station Futenma to Henoko Bay in northern Okinawa Island.