It follows 0.8 percent growth for the first quarter and marks the weakest since a 0.3 percent gain in the last quarter of 2014.
It was also slightly below a 0.4 percent gain tipped in a Reuters survey of 20 analysts on a seasonally adjusted basis.
The Bank of Korea estimates showed private consumption fell by a seasonally adjusted 0.3 percent in the second quarter after rising 0.6 percent in the January-March period.
Capital investment notched a 0.4 percent gain after a 0.2 percent rise.
Asia's fourth-largest economy, which relies heavily on exports, has been suffering from poor global demand as well as sluggish consumption brought on by the spread of MERS, which led to massive travel cancellations especially by foreign tourists.
The economy expanded 2.2 percent in the June quarter from a year earlier, compared with a median 2.3 percent forecast in the Reuters poll and 2.5 percent growth in the first quarter.