The boy was playing near the 30-inch pipe when rushing rainwater water swept him into it and carried him underground.
His father found the child when the current eventually carried him out of the pipe.
The child was unresponsive when emergency workers arrived at the scene near Walmart on Highway 51.
They administered CPR and rushed the boy to Le Bonheur Children's Medical Center, where he later died.
Witnesses said the he lived in the Westside Community trailer park - just steps from the large culvert, which belongs to Wal-Mart.
Neighbors say the large pipe should have been covered by a grate.
"I've never seen a culvert in my life that didn't have a grate or something in front of it to keep debris - and especially little children - from going into it," said neighbor Gerald Scalf.
Wal-Mart had no comment Sunday.