Exports were boosted by rising shipments of vehicles, iron and steel, rubber, chemicals and machinery.
The U.S. remained Japan's largest export destination, at 1.11 trillion yen ($11.3 billion), while imports totaled 665 billion yen ($6.8 billion). The resulting 533 billion yen ($5.4 billion) surplus rose 25 percent from a year earlier.
But Japan's trade deficit with China jumped 87 percent to 620 billion yen ($6.3 billion) as imports of such items as cellphones and solar panels surged 31 percent to 1.68 trillion yen ($17 billion) while exports were up 11 percent at 1.06 trillion yen ($10.8 billion).
Japan's shipments to China, Japan's biggest trade partner, grew 11.4 percent to 1.06 trillion yen in September, while imports from China soared 30.9 percent to 1.68 trillion yen.