Yushchenko signed the agreement on WTO backing at a meeting with Prime Minister Junichiro Koizumi after political unrest at home over Ukraine's bid to enter the world trade body.
Koizumi and Yushchenko "welcomed the conclusion of the bilateral negotiations between Japan and Ukraine (on) the WTO and expressed their hope for the early accession of Ukraine," a joint statement said.
Joining the WTO "would further promote the integration of Ukraine into the world community," it said.
Ukraine has finished WTO accession negotiations with the European Union, which it also wants to join, but the United States has said Kiev must first take further measures to conform to world trade rules.
The Ukrainian parliament descended into chaos including fistfights when it took up WTO accession earlier this month, passing only half of the necessary bills before adjourning for summer recess.
Yushchenko had hoped for approval of the bills to show the international community Ukraine's pro-Western ambitions and set the state for its accession at a WTO ministerial meeting in Hong Kong in December.
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