The rise in exports compared with expectations of a 15.6 percent increase according to a Reuters poll of economists.
Imports rose 16.5 percent in September from a year earlier, versus a 20.0 percent increase expected, partly as a weaker yen inflated the cost of importing fossil fuels.
Higher import costs resulted in a trade deficit of 932.1 billion yen ($9.5 billion) compared with the median estimate for a 920 billion yen deficit. It was a record 15th straight month of deficits.
On a seasonally adjusted basis, Japan's exports fell 0.3 percent in September from the previous month.