Lee Hee-Ho's four-day visit was ostensibly humanitarian but there had been much speculation about a possible meeting with Kim, who personally invited her.
However, her aides said she had had no chance of seeing the young leader during the trip.
Lee's husband is best remembered for his "sunshine" policy of engagement with the isolated but nuclear-armed North that led to a historic summit between him and Kim Jong-Un's late father Kim Jong-Il in 2000.
"However, I made the trip with a view to dedicating to the spirit of the June 15 declaration", she said in a statement on returning to Seoul, referring to an inter-Korean agreement for peace and reconciliation signed at the end of the landmark summit.
After arriving in Pyongyang, Lee had visited hospitals caring for children and young mothers.
"Holding the hands of innocent, beaming children there, I deeply felt we should not pass the pain of the division of the motherland on to the next generations", she said.
The "sunshine" policy was largely abandoned when a conservative administration took power in South Korea in 2008 and cross-border ties soured.
A series of nuclear and missile launches by the North in recent years as well as occasional military clashes have kept tensions high.
Lee had visited the North three times before, the last trip being to pay respects during the funeral of Kim Jong-Il in December 2011.
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